diff --git a/.classpath b/.classpath index 9527d1e0..7b824e4a 100755 --- a/.classpath +++ b/.classpath @@ -1,690 +1,25 @@ - + + + - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + diff --git a/.github/workflows/build-gradle-project.yml b/.github/workflows/build-gradle-project.yml index 73c43fec..5e76c456 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: 3.1.0 + IMAGE_TAG: 3.3.0 runs-on: ubuntu-latest steps: - name: Get branch names diff --git a/.java-version b/.java-version index b4de3947..f222bf6f 100644 --- a/.java-version +++ b/.java-version @@ -1 +1 @@ -11 +21.0.4 diff --git a/Dockerfile b/Dockerfile index e6095937..35a3c349 100755 --- a/Dockerfile +++ b/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 diff --git a/build.gradle b/build.gradle index 77326569..d857d686 100755 --- a/build.gradle +++ b/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' diff --git a/changelog.md b/changelog.md index 39269a71..bafa3230 100644 --- a/changelog.md +++ b/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 diff --git a/src/main/java/org/kpmp/Application.java b/src/main/java/org/kpmp/Application.java index d6afb2a3..4d92991b 100755 --- a/src/main/java/org/kpmp/Application.java +++ b/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); + } } \ No newline at end of file diff --git a/src/main/java/org/kpmp/QueryController.java b/src/main/java/org/kpmp/QueryController.java index 50cc7fb4..335b1931 100755 --- a/src/main/java/org/kpmp/QueryController.java +++ b/src/main/java/org/kpmp/QueryController.java @@ -3,6 +3,7 @@ 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; @@ -10,6 +11,8 @@ 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; @@ -17,19 +20,9 @@ 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; @@ -45,41 +38,35 @@ 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 @@ -87,29 +74,11 @@ public List autocomplete(@Argument String searchTerm) throws 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 geneExpressionSummary(@Argument String dataType, @Argument String geneSymbol, - @Argument String cellType, @Argument String enrollmentCategory) throws IOException { - List 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 geneExpressionSummary2025(@Argument String dataType, @Argument String geneSymbol, @Argument String cellType, @Argument String enrollmentCategory) throws IOException { @@ -123,26 +92,11 @@ public List geneExpressionSummary2025(@Argument return results; } - @QueryMapping - public List getClusterHieararchies(@Argument String cellType) throws IOException { - return clusterHierarchyService.findClustersByCellType(cellType); - } - @QueryMapping public List 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 getDataTypeSummaryInformation() throws Exception { - try { - return geneExpressionSummaryService.getDataTypeSummaryInformation(); - } catch (Exception e) { - logger.error(e.getMessage()); - throw e; - } - } - @QueryMapping public List getDataTypeSummaryInformation2025() throws Exception { try { @@ -183,21 +127,10 @@ public List getSummaryData() throws Exception { } } - @QueryMapping - public List 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 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 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 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 getAtlasMessages() throws Exception { @QueryMapping public List getExperimentalStrategyCountsByParticipant(@Argument String redcapId) { - return participantService.getExperimentalStrategyCountsByParticipant(redcapId); + return participantService2025.getExperimentalStrategyCountsByParticipant(redcapId); + } + + @QueryMapping + public List getHubmapTermMap() { + return hubmapCellTypeMappingService.buildHubmapIdToCellTypeMap(); } } \ No newline at end of file diff --git a/src/main/java/org/kpmp/cellType/CellTypeRepository.java b/src/main/java/org/kpmp/cellType/CellTypeRepository.java index 4d3c7a28..eca40027 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeRepository.java +++ b/src/main/java/org/kpmp/cellType/CellTypeRepository.java @@ -19,9 +19,6 @@ public interface CellTypeRepository extends CrudRepository { + " WHERE ct.cell_type LIKE %:searchTerm% ", nativeQuery = true) List findByCellTypeContainingOrSynonymContaining(@Param("searchTerm") String searchTerm); - @Cacheable("cellTypeIsNotNullOrderByCellTypeOrdering") - List 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 findAllByCellTypeIsNotNullOrderByCellTypeOrdering2025(); diff --git a/src/main/java/org/kpmp/cellType/CellTypeService.java b/src/main/java/org/kpmp/cellType/CellTypeService.java index 744f781f..f9c5712e 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeService.java +++ b/src/main/java/org/kpmp/cellType/CellTypeService.java @@ -15,21 +15,6 @@ public CellTypeService(CellTypeRepository cellTypeRepo) { this.cellTypeRepo = cellTypeRepo; } - public CellTypeHierarchy getCellTypeHierarchy() { - List 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 cellTypes = cellTypeRepo.findAllByCellTypeIsNotNullOrderByCellTypeOrdering2025(); CellTypeHierarchy hierarchy = new CellTypeHierarchy(); diff --git a/src/main/java/org/kpmp/cellType/HubmapCellTypeMappingService.java b/src/main/java/org/kpmp/cellType/HubmapCellTypeMappingService.java new file mode 100644 index 00000000..9e059016 --- /dev/null +++ b/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 buildHubmapIdToCellTypeMap() { + return repo.findAll(); + } +} diff --git a/src/main/java/org/kpmp/cellType/HubmapOnotologyCellTypeRepository.java b/src/main/java/org/kpmp/cellType/HubmapOnotologyCellTypeRepository.java new file mode 100644 index 00000000..9052121c --- /dev/null +++ b/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 { + + @NotNull + @Cacheable("hubmapOntologyCellTypeMap") + List findAll(); +} diff --git a/src/main/java/org/kpmp/cellType/HubmapOntologyCellType.java b/src/main/java/org/kpmp/cellType/HubmapOntologyCellType.java new file mode 100644 index 00000000..6d1f56b5 --- /dev/null +++ b/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; + } + +} diff --git a/src/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.java b/src/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.java index 8df0a5c1..2024d666 100755 --- a/src/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.java +++ b/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; @@ -10,10 +9,6 @@ interface ClusterHiearchyRepository extends CrudRepository { - @Override - @Cacheable("clusterHierarchy") - List findAll(); - @Cacheable("clusterHierarchyRNA2025ByCellType") @Query(value = "SELECT ch.*, 'N' AS is_rt, 'N' AS is_rp FROM cluster_hierarchy_2025_v ch WHERE ch.cell_type = :cell_type OR ch.structure_region = :cell_type OR ch.structure_subregion = :cell_type " + "ORDER BY ch.cell_type_order ASC", nativeQuery = true) @@ -54,12 +49,4 @@ interface ClusterHiearchyRepository extends CrudRepository findByCellType(@Param("cell_type") String cellType); - - @Cacheable("clusterHierarchyCluster") - @Query(value = "CALL cluster_hierarchy_by_cluster_sp(:cluster);", nativeQuery = true) - ClusterHierarchy findFirstByClusterOrRegion(String cluster); - } diff --git a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java index c633a9f1..adc7f6bb 100755 --- a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java +++ b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java @@ -7,8 +7,10 @@ import jakarta.persistence.Id; import jakarta.persistence.IdClass; import jakarta.persistence.Table; +import jakarta.persistence.Transient; import org.springframework.lang.Nullable; +import com.fasterxml.jackson.annotation.JsonProperty; @Entity @Table(name = "cluster_hierarchy_v") @@ -42,6 +44,9 @@ public class ClusterHierarchy implements Serializable { @Column(name = "cell_type_order") private Double cellTypeOrder; + @Transient + private String isSpatialTranscriptomics; + public int getCellTypeId() { return cellTypeId; } @@ -116,6 +121,16 @@ public String getIsRegionalProteomics() { public void setIsRegionalProteomics(String isRegionalProteomics) { this.isRegionalProteomics = isRegionalProteomics; } + + @JsonProperty("isSpatialTranscriptomics") + public String getIsSpatialTranscriptomics() { + return isSpatialTranscriptomics; + } + + public void setIsSpatialTranscriptomics(String isSpatialTranscriptomics) { + this.isSpatialTranscriptomics = isSpatialTranscriptomics; + } + @Nullable public Double getCellTypeOrder() { return cellTypeOrder; diff --git a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy2025.java b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy2025.java deleted file mode 100644 index f7202195..00000000 --- a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy2025.java +++ /dev/null @@ -1,130 +0,0 @@ -package org.kpmp.cellTypeSummary; - -import jakarta.persistence.*; -import org.springframework.lang.Nullable; - -import java.io.Serializable; - -@Entity -@Table(name = "cluster_hierarchy_2025_v") -@IdClass(ClusterHierarchyId.class) -public class ClusterHierarchy2025 implements Serializable { - - private static final long serialVersionUID = -7707637379989017634L; - @Id - @Column(name = "cell_type_id") - private int cellTypeId; - @Id - @Column(name = "cluster_id") - private int clusterId; - @Column(name = "structure_region") - private String structureRegion; - @Column(name = "structure_subregion") - private String structureSubregion; - @Column(name = "cluster_name") - private String clusterName; - @Column(name = "is_single_cell") - private String isSingleCellCluster; - @Column(name = "is_single_nuc") - private String isSingleNucCluster; - @Column(name = "is_rt") - private String isRegionalTranscriptomics; - @Column(name = "is_rp") - private String isRegionalProteomics; - @Column(name = "cell_type") - private String cellType; - @Column(name = "cell_type_order") - private Double cellTypeOrder; - - public int getCellTypeId() { - return cellTypeId; - } - - public void setCellTypeId(int cellTypeId) { - this.cellTypeId = cellTypeId; - } - - @Nullable - public int getClusterId() { - return clusterId; - } - - public void setClusterId(int clusterId) { - this.clusterId = clusterId; - } - - public String getStructureRegion() { - return structureRegion; - } - - public void setStructureRegion(String structureRegion) { - this.structureRegion = structureRegion; - } - - @Nullable - public String getStructureSubregion() { - return structureSubregion; - } - - public void setStructureSubregion(String structureSubregion) { - this.structureSubregion = structureSubregion; - } - - @Nullable - public String getClusterName() { - return clusterName; - } - - public void setClusterName(String clusterName) { - this.clusterName = clusterName; - } - - public String getIsSingleCellCluster() { - return isSingleCellCluster; - } - - public void setIsSingleCellCluster(String isSingleCellCluster) { - this.isSingleCellCluster = isSingleCellCluster; - } - - public String getIsSingleNucCluster() { - return isSingleNucCluster; - } - - public void setIsSingleNucCluster(String isSingleNucCluster) { - this.isSingleNucCluster = isSingleNucCluster; - } - - public String getIsRegionalTranscriptomics() { - return isRegionalTranscriptomics; - } - - public void setIsRegionalTranscriptomics(String isRegionalTranscriptomics) { - this.isRegionalTranscriptomics = isRegionalTranscriptomics; - } - - public String getIsRegionalProteomics() { - return isRegionalProteomics; - } - - public void setIsRegionalProteomics(String isRegionalProteomics) { - this.isRegionalProteomics = isRegionalProteomics; - } - @Nullable - public Double getCellTypeOrder() { - return cellTypeOrder; - } - - public void setCellTypeOrder(Double cellTypeOrder) { - this.cellTypeOrder = cellTypeOrder; - } - - @Nullable - public String getCellType() { - return cellType; - } - - public void setCellType(String cellType) { - this.cellType = cellType; - } -} diff --git a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchyService.java b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchyService.java index 46bfb1ea..3155e47f 100755 --- a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchyService.java +++ b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchyService.java @@ -16,66 +16,6 @@ public ClusterHierarchyService(ClusterHiearchyRepository clusterHierarchyRepo) { this.clusterHierarchyRepo = clusterHierarchyRepo; } - public List findClustersByCellType(String cellType) { - - ArrayList result = new ArrayList<>(); - Map clusterToHierarchy = new HashMap<>(); - List clusterHierarchies = clusterHierarchyRepo.findByCellType(cellType); - for (ClusterHierarchy clusterHierarchy : clusterHierarchies) { - String clusterName = clusterHierarchy.getClusterName(); - if (clusterToHierarchy.containsKey(clusterName)) { - if (clusterName == null) { - result.add(clusterHierarchy); - } else if (clusterName != null && clusterName.equals(clusterHierarchy.getCellType())) { - clusterToHierarchy.put(clusterName, clusterHierarchy); - } - } else { - clusterToHierarchy.put(clusterName, clusterHierarchy); - } - } - if (cellType.equals("Tubules") || cellType.equals("Interstitium")) { - ClusterHierarchy tiCluster = new ClusterHierarchy(); - tiCluster.setStructureRegion("Tubulo-interstitium"); - tiCluster.setIsSingleCellCluster("N"); - tiCluster.setIsSingleNucCluster("N"); - tiCluster.setIsRegionalProteomics("Y"); - tiCluster.setIsRegionalTranscriptomics("Y"); - tiCluster.setCellTypeOrder(0.01); - result.add(tiCluster); - } - result.addAll(clusterToHierarchy.values()); - Collections.sort(result, new Comparator() { - @Override - public int compare(ClusterHierarchy a, ClusterHierarchy b) { - return a.getCellTypeOrder().compareTo(b.getCellTypeOrder()); - } - }); - return result; - } - - public List findDataTypesByClusterName(String clusterName) { - List dataTypesRepresented = new ArrayList<>(); - if (clusterName.equals("Tubulo-interstitium")) { - dataTypesRepresented.add(FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation()); - dataTypesRepresented.add(FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation()); - } else { - ClusterHierarchy clustersInDataTypes = clusterHierarchyRepo.findFirstByClusterOrRegion(clusterName); - if (clustersInDataTypes.getIsSingleCellCluster().equalsIgnoreCase("Y")) { - dataTypesRepresented.add(FullDataTypeEnum.SINGLE_CELL.getAbbreviation()); - } - if (clustersInDataTypes.getIsSingleNucCluster().equalsIgnoreCase("Y")) { - dataTypesRepresented.add(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()); - } - if (clustersInDataTypes.getIsRegionalTranscriptomics().equalsIgnoreCase("Y")) { - dataTypesRepresented.add(FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation()); - } - if (clustersInDataTypes.getIsRegionalProteomics().equalsIgnoreCase("Y")) { - dataTypesRepresented.add(FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation()); - } - } - return dataTypesRepresented; - } - public List findClustersByCellType2025(String cellType) { ArrayList result = new ArrayList<>(); @@ -84,6 +24,7 @@ public List findClustersByCellType2025(String cellType) { List clusterHierarchiesRNASeq = clusterHierarchyRepo.findRnaSeqByCellTypeOrRegion(cellType); List clusterHierarchiesRegional = clusterHierarchyRepo.findRTRPByCellTypeOrRegion(cellType); List clusterHierarchiesParentRegions = clusterHierarchyRepo.findRTRPParentRegions(cellType); + clusterHierarchiesRNASeq.addAll(clusterHierarchiesRegional); clusterHierarchiesRNASeq.addAll(clusterHierarchiesParentRegions); clusterHierarchySet.addAll(clusterHierarchiesRNASeq); @@ -109,6 +50,15 @@ public List findClustersByCellType2025(String cellType) { tiCluster.setCellTypeOrder(0.01); result.add(tiCluster); } + ClusterHierarchy bogusST = new ClusterHierarchy(); + bogusST.setIsSpatialTranscriptomics("Y"); + bogusST.setCellTypeOrder(-1.0); + bogusST.setIsSingleCellCluster("N"); + bogusST.setIsSingleNucCluster("N"); + bogusST.setIsRegionalProteomics("N"); + bogusST.setIsRegionalTranscriptomics("N"); + bogusST.setStructureRegion("Glomerulus / Renal Corpuscle"); + result.add(bogusST); result.addAll(clusterToHierarchy.values()); Collections.sort(result, new Comparator() { @Override diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java index d34beb59..f5d905f9 100755 --- a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java @@ -1,148 +1,148 @@ -package org.kpmp.geneExpression; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.Table; - -@Entity -@Table(name = "rt_segments") -public class RTExpressionDataAllSegments implements RTExpressionData, Serializable { - - private static final long serialVersionUID = 9029734049386312455L; - @Id - @Column(name = "id") - private Integer id; - @Column(name = "gene_symbol") - private String geneSymbol; - @Column(name = "segment") - private String segment; - @Column(name = "segment_name") - private String segmentName; - @Column(name = "fold_change") - private Double foldChange; - @Column(name = "p_val") - private Double pVal; - @Column(name = "std_dev") - private Double stdDev; - @Column(name = "p_val_log10") - private Double pValLog10; - @Column(name = "enrollment_category") - private String enrollmentCategory; - @Column(name = "adj_p_val") - private Double adjPVal; - @Column(name = "sample_count") - private Integer sampleCount; - - @Override - public Integer getId() { - return id; - } - - @Override - public void setId(Integer id) { - this.id = id; - } - - @Override - public String getGeneSymbol() { - return geneSymbol; - } - - @Override - public void setGeneSymbol(String geneSymbol) { - this.geneSymbol = geneSymbol; - } - - @Override - public String getSegment() { - return segment; - } - - @Override - public void setSegment(String segment) { - this.segment = segment; - } - - @Override - public Double getFoldChange() { - return foldChange; - } - - @Override - public void setFoldChange(Double foldChange) { - this.foldChange = foldChange; - } - - @Override - public Double getPVal() { - return pVal; - } - - @Override - public void setPVal(Double pVal) { - this.pVal = pVal; - } - - @Override - public Double getStdDev() { - return stdDev; - } - - @Override - public void setStdDev(Double stdDev) { - this.stdDev = stdDev; - } - - @Override - public Double getPValLog10() { - return pValLog10; - } - - @Override - public void setPValLog10(Double pValLog10) { - this.pValLog10 = pValLog10; - } - - @Override - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - @Override - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } - - @Override - public Integer getSampleCount() { - return sampleCount; - } - - @Override - public void setSampleCount(Integer sampleCount) { - this.sampleCount = sampleCount; - } - - @Override - public String getSegmentName() { - return segmentName; - } - - @Override - public void setSegmentName(String segmentName) { - this.segmentName = segmentName; - } - - @Override - public Double getAdjPVal() { - return adjPVal; - } - - @Override - public void setAdjPVal(Double adjPVal) { - this.adjPVal = adjPVal; - } -} +package org.kpmp.geneExpression; + +import java.io.Serializable; + +import jakarta.persistence.*; + +@Entity +@Table(name = "rt_segments") +@IdClass(RTExpressionDataId.class) +public class RTExpressionDataAllSegments implements RTExpressionData, Serializable { + + private static final long serialVersionUID = 9029734049386312455L; + @Id + @Column(name = "id") + private Integer id; + @Id + @Column(name = "gene_symbol") + private String geneSymbol; + @Column(name = "segment") + private String segment; + @Column(name = "segment_name") + private String segmentName; + @Column(name = "fold_change") + private Double foldChange; + @Id + @Column(name = "p_val") + private Double pVal; + @Column(name = "std_dev") + private Double stdDev; + @Column(name = "p_val_log10") + private Double pValLog10; + @Column(name = "enrollment_category") + private String enrollmentCategory; + @Column(name = "adj_p_val") + private Double adjPVal; + @Column(name = "sample_count") + private Integer sampleCount; + + @Override + public Integer getId() { + return id; + } + + @Override + public void setId(Integer id) { + this.id = id; + } + + @Override + public String getGeneSymbol() { + return geneSymbol; + } + + @Override + public void setGeneSymbol(String geneSymbol) { + this.geneSymbol = geneSymbol; + } + + @Override + public String getSegment() { + return segment; + } + + @Override + public void setSegment(String segment) { + this.segment = segment; + } + + @Override + public Double getFoldChange() { + return foldChange; + } + + @Override + public void setFoldChange(Double foldChange) { + this.foldChange = foldChange; + } + + @Override + public Double getPVal() { + return pVal; + } + + @Override + public void setPVal(Double pVal) { + this.pVal = pVal; + } + + @Override + public Double getStdDev() { + return stdDev; + } + + @Override + public void setStdDev(Double stdDev) { + this.stdDev = stdDev; + } + + @Override + public Double getPValLog10() { + return pValLog10; + } + + @Override + public void setPValLog10(Double pValLog10) { + this.pValLog10 = pValLog10; + } + + @Override + public String getEnrollmentCategory() { + return enrollmentCategory; + } + + @Override + public void setEnrollmentCategory(String enrollmentCategory) { + this.enrollmentCategory = enrollmentCategory; + } + + @Override + public Integer getSampleCount() { + return sampleCount; + } + + @Override + public void setSampleCount(Integer sampleCount) { + this.sampleCount = sampleCount; + } + + @Override + public String getSegmentName() { + return segmentName; + } + + @Override + public void setSegmentName(String segmentName) { + this.segmentName = segmentName; + } + + @Override + public Double getAdjPVal() { + return adjPVal; + } + + @Override + public void setAdjPVal(Double adjPVal) { + this.adjPVal = adjPVal; + } +} diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsRepository.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsRepository.java index 7227691e..79a5d5e5 100755 --- a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsRepository.java +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsRepository.java @@ -9,7 +9,7 @@ import org.springframework.stereotype.Repository; @Repository -public interface RTExpressionDataAllSegmentsRepository extends CrudRepository { +public interface RTExpressionDataAllSegmentsRepository extends CrudRepository { @Cacheable("rtExpGeneSymbolAndEnrollmentCategoryWithCounts") @Query(value = "SELECT rts.*, rsv.sample_count, s.segment_name FROM rt_segments rts " + "LEFT JOIN rt_summary_v rsv ON rts.segment = rsv.segment AND rts.enrollment_category = rsv.enrollment_category " diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataId.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataId.java new file mode 100644 index 00000000..88c78d2e --- /dev/null +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataId.java @@ -0,0 +1,39 @@ +package org.kpmp.geneExpression; + +import java.io.Serializable; +import java.util.Objects; + +public class RTExpressionDataId implements Serializable { + + private Integer id; + private String geneSymbol; + private Double pVal; + + public RTExpressionDataId() {} + + public RTExpressionDataId(Integer id, String geneSymbol, Double pVal) { + this.id = id; + this.geneSymbol = geneSymbol; + this.pVal = pVal; + } + + public Integer getId() { return id; } + public void setId(Integer id) { this.id = id; } + public String getGeneSymbol() { return geneSymbol; } + public void setGeneSymbol(String geneSymbol) { this.geneSymbol = geneSymbol; } + public Double getPVal() { return pVal; } + public void setPVal(Double pVal) { this.pVal = pVal; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + RTExpressionDataId that = (RTExpressionDataId) o; + return Objects.equals(id, that.id) && Objects.equals(geneSymbol, that.geneSymbol) && Objects.equals(pVal, that.pVal); + } + + @Override + public int hashCode() { + return Objects.hash(id, geneSymbol, pVal); + } +} diff --git a/src/main/java/org/kpmp/geneExpression/SCExpressionData.java b/src/main/java/org/kpmp/geneExpression/SCExpressionData.java deleted file mode 100755 index 9b40ab04..00000000 --- a/src/main/java/org/kpmp/geneExpression/SCExpressionData.java +++ /dev/null @@ -1,45 +0,0 @@ -package org.kpmp.geneExpression; - -import java.io.Serializable; - -import org.json.JSONException; -import org.json.JSONObject; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.Table; - - -@Entity -@Table(name = "sc_feature_data") -class SCExpressionData implements Serializable { - - private static final long serialVersionUID = 1079445825708102694L; - @Id - @Column(name = "gene_symbol") - private String geneSymbol; - @Column(name = "expression_data") - private String expressionString; - - public String getGeneSymbol() { - return geneSymbol; - } - - public void setGeneSymbol(String geneSymbol) { - this.geneSymbol = geneSymbol; - } - - public String getExpressionString() { - return expressionString; - } - - public void setExpressionString(String expressionString) { - this.expressionString = expressionString; - } - - public JSONObject getExpressionDataAsJson() throws JSONException { - return new JSONObject(expressionString); - } - -} diff --git a/src/main/java/org/kpmp/geneExpression/SCExpressionDataRepository.java b/src/main/java/org/kpmp/geneExpression/SCExpressionDataRepository.java deleted file mode 100755 index 558986a3..00000000 --- a/src/main/java/org/kpmp/geneExpression/SCExpressionDataRepository.java +++ /dev/null @@ -1,11 +0,0 @@ -package org.kpmp.geneExpression; - -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.repository.CrudRepository; - -interface SCExpressionDataRepository extends CrudRepository { - - @Cacheable("scExpression") - SCExpressionData findByGeneSymbol(String geneSymbol); - -} diff --git a/src/main/java/org/kpmp/geneExpression/SNExpressionData.java b/src/main/java/org/kpmp/geneExpression/SNExpressionData.java deleted file mode 100755 index a8cecf64..00000000 --- a/src/main/java/org/kpmp/geneExpression/SNExpressionData.java +++ /dev/null @@ -1,44 +0,0 @@ -package org.kpmp.geneExpression; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.Table; - -import org.json.JSONException; -import org.json.JSONObject; - -@Entity -@Table(name = "sn_feature_data") -public class SNExpressionData implements Serializable { - - private static final long serialVersionUID = -3363426907715685587L; - @Id - @Column(name = "gene_symbol") - private String geneSymbol; - @Column(name = "expression_data") - private String expressionString; - - public String getGeneSymbol() { - return geneSymbol; - } - - public void setGeneSymbol(String geneSymbol) { - this.geneSymbol = geneSymbol; - } - - public String getExpressionString() { - return expressionString; - } - - public void setExpressionString(String expressionString) { - this.expressionString = expressionString; - } - - public JSONObject getExpressionDataAsJson() throws JSONException { - return new JSONObject(expressionString); - } - -} diff --git a/src/main/java/org/kpmp/geneExpression/SNExpressionDataRepository.java b/src/main/java/org/kpmp/geneExpression/SNExpressionDataRepository.java deleted file mode 100755 index a3061cd7..00000000 --- a/src/main/java/org/kpmp/geneExpression/SNExpressionDataRepository.java +++ /dev/null @@ -1,11 +0,0 @@ -package org.kpmp.geneExpression; - -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.repository.CrudRepository; - -interface SNExpressionDataRepository extends CrudRepository { - - @Cacheable("snExpression") - SNExpressionData findByGeneSymbol(String geneSymbol); - -} diff --git a/src/main/java/org/kpmp/geneExpression/SNSCExpressionDataService.java b/src/main/java/org/kpmp/geneExpression/SNSCExpressionDataService.java deleted file mode 100755 index 89b31172..00000000 --- a/src/main/java/org/kpmp/geneExpression/SNSCExpressionDataService.java +++ /dev/null @@ -1,32 +0,0 @@ -package org.kpmp.geneExpression; - -import org.json.JSONException; -import org.json.JSONObject; -import org.kpmp.FullDataTypeEnum; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; - -@Service -public class SNSCExpressionDataService { - - private SNExpressionDataRepository snRepo; - private SCExpressionDataRepository scRepo; - - @Autowired - public SNSCExpressionDataService(SNExpressionDataRepository snRepo, SCExpressionDataRepository scRepo) { - this.snRepo = snRepo; - this.scRepo = scRepo; - } - - public JSONObject getGeneExpressionValues(String dataType, String geneSymbol) throws JSONException, Exception { - if (dataType.equals(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation())) { - SNExpressionData expressionData = snRepo.findByGeneSymbol(geneSymbol); - return expressionData.getExpressionDataAsJson(); - } else if (dataType.equals(FullDataTypeEnum.SINGLE_CELL.getAbbreviation())) { - SCExpressionData expressionData = scRepo.findByGeneSymbol(geneSymbol); - return expressionData.getExpressionDataAsJson(); - } - throw new Exception("Invalid data type: " + dataType); - } - -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java deleted file mode 100755 index 341ba9f0..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java +++ /dev/null @@ -1,201 +0,0 @@ -package org.kpmp.geneExpressionSummary; - -import java.util.ArrayList; -import java.util.List; -import java.util.stream.Collectors; - -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; -import org.kpmp.geneExpressionSummary.regionalProteomics.RPParticipantRepository; -import org.kpmp.geneExpressionSummary.regionalTranscriptomics.RTParticipantRepository; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionSummaryRepository; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionSummaryRepository2025; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAParticipantRepository; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionSummaryRepository; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionSummaryRepository2025; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAParticipantRepository; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; - -@Service -public class GeneExpressionSummaryService { - private SCRNAGeneExpressionSummaryRepository scrnaGeneExpressionRepository; - private SNRNAGeneExpressionSummaryRepository snrnaGeneExpressionRepository; - private SCRNAGeneExpressionSummaryRepository2025 scrnaGeneExpressionRepository2025; - private SNRNAGeneExpressionSummaryRepository2025 snrnaGeneExpressionRepository2025; - private SCRNAParticipantRepository scrnaParticipantRepository; - private SNRNAParticipantRepository snrnaParticipantRepository; - private RTParticipantRepository rtParticipantRepository; - - private RPParticipantRepository rpParticipantRepository; - private RPExpressionDataRepository rpExpressionDataRepository; - RTExpressionDataAllSegmentsRepository rtExpressionDataAllSegmentsRepository; - - @Autowired - public GeneExpressionSummaryService(SCRNAGeneExpressionSummaryRepository scrnaGeneExpressionRepository, - SNRNAGeneExpressionSummaryRepository snrnaGeneExpressionRepository, - SNRNAGeneExpressionSummaryRepository2025 snrnaGeneExpressionRepository2025, - SCRNAParticipantRepository scrnaParticipantRepository, - SCRNAGeneExpressionSummaryRepository2025 scrnaGeneExpressionRepository2025, - SNRNAParticipantRepository snrnaParticipantRepository, RTParticipantRepository rtParticipantRepository, - RTExpressionDataAllSegmentsRepository rtExpressionDataAllSegmentsRepository, RPExpressionDataRepository rpExpressionDataRepository, RPParticipantRepository rpParticipantRepository) { - this.scrnaGeneExpressionRepository = scrnaGeneExpressionRepository; - this.snrnaGeneExpressionRepository = snrnaGeneExpressionRepository; - this.snrnaGeneExpressionRepository2025 = snrnaGeneExpressionRepository2025; - this.scrnaGeneExpressionRepository2025 = scrnaGeneExpressionRepository2025; - this.scrnaParticipantRepository = scrnaParticipantRepository; - this.snrnaParticipantRepository = snrnaParticipantRepository; - this.rtParticipantRepository = rtParticipantRepository; - this.rpExpressionDataRepository = rpExpressionDataRepository; - this.rpParticipantRepository = rpParticipantRepository; - this.rtExpressionDataAllSegmentsRepository = rtExpressionDataAllSegmentsRepository; - } - - public List getByDataTypeEnrollmentCategoryAndGene(String dataType, String geneSymbol, - String enrollmentCategory) { - List results = new ArrayList<>(); - FullDataTypeEnum dataTypeEnum = FullDataTypeEnum.fromAbbreviation(dataType); - EnrollmentCategoryEnum enrollmentCategoryEnum = EnrollmentCategoryEnum.fromRequestType(enrollmentCategory); - switch (dataTypeEnum) { - case SINGLE_CELL: - return scrnaGeneExpressionRepository - .findByEnrollmentAndGeneAllClusters(geneSymbol, enrollmentCategoryEnum.getParticipantEnrollmentCategory()).stream() - .distinct().collect(Collectors.toList()); - case SINGLE_NUCLEUS: - return snrnaGeneExpressionRepository - .findByEnrollmentAndGeneAllClusters(geneSymbol, enrollmentCategoryEnum.getParticipantEnrollmentCategory()).stream() - .distinct().collect(Collectors.toList()); - case UNKNOWN: - List allResults = new ArrayList<>(); - allResults.addAll(scrnaGeneExpressionRepository.findByEnrollmentAndGeneAllClusters(geneSymbol, - enrollmentCategoryEnum.getParticipantEnrollmentCategory())); - allResults.addAll(snrnaGeneExpressionRepository.findByEnrollmentAndGeneAllClusters(geneSymbol, - enrollmentCategoryEnum.getParticipantEnrollmentCategory())); - return allResults; - default: - break; - - } - return results; - } - - @SuppressWarnings({ "rawtypes", "unchecked" }) - public List getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory(String dataType, - String cellType, String enrollmentCategory) { - List results = new ArrayList<>(); - FullDataTypeEnum dataTypeEnum = FullDataTypeEnum.fromAbbreviation(dataType); - EnrollmentCategoryEnum enrollmentCategoryEnum = EnrollmentCategoryEnum.fromRequestType(enrollmentCategory); - switch (dataTypeEnum) { - case SINGLE_CELL: - results = scrnaGeneExpressionRepository.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory(cellType, - enrollmentCategoryEnum.getParticipantEnrollmentCategory()); - break; - case SINGLE_NUCLEUS: - results = snrnaGeneExpressionRepository.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory(cellType, - enrollmentCategoryEnum.getParticipantEnrollmentCategory()); - break; - case UNKNOWN: - List allResults = new ArrayList<>(); - allResults.addAll(scrnaGeneExpressionRepository.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory( - cellType, enrollmentCategoryEnum.getParticipantEnrollmentCategory())); - allResults.addAll(snrnaGeneExpressionRepository.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory( - cellType, enrollmentCategoryEnum.getParticipantEnrollmentCategory())); - results = allResults; - default: - break; - } - return results; - } - - public List findDataTypesByGene2025(String gene) { - List dataTypes = new ArrayList<>(); - long scCountByGene = scrnaGeneExpressionRepository2025.getCountByGene(gene); - if (scCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.SINGLE_CELL.getAbbreviation()); - } - - long snCountByGene = snrnaGeneExpressionRepository2025.getCountByGene(gene); - if (snCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()); - } - long rtCountByGene = rtExpressionDataAllSegmentsRepository.getCountByGene(gene); - if (rtCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation()); - } - long rpCountByGene = rpExpressionDataRepository.getCountByGene(gene); - if (rpCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation()); - } - return dataTypes; - } - - public List findDataTypesByGene(String gene) { - List dataTypes = new ArrayList<>(); - long scCountByGene = scrnaGeneExpressionRepository.getCountByGene(gene); - if (scCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.SINGLE_CELL.getAbbreviation()); - } - - long snCountByGene = snrnaGeneExpressionRepository.getCountByGene(gene); - if (snCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()); - } - long rtCountByGene = rtExpressionDataAllSegmentsRepository.getCountByGene(gene); - if (rtCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation()); - } - long rpCountByGene = rpExpressionDataRepository.getCountByGene(gene); - if (rpCountByGene != 0) { - dataTypes.add(FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation()); - } - return dataTypes; - } - - public List getDataTypeSummaryInformation() { - List dataTypeSummary = new ArrayList<>(); - dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.SINGLE_CELL.getFullName(), FullDataTypeEnum.SINGLE_CELL.getAbbreviation(), - scrnaGeneExpressionRepository.getCountByEnrollment(EnrollmentCategoryEnum.AKI.getParticipantEnrollmentCategory()), - scrnaGeneExpressionRepository.getCountByEnrollment(EnrollmentCategoryEnum.CKD.getParticipantEnrollmentCategory()), - scrnaGeneExpressionRepository - .getCountByEnrollment(EnrollmentCategoryEnum.HEALTHY_REFERENCE.getParticipantEnrollmentCategory()), - scrnaGeneExpressionRepository.getCountByEnrollment(EnrollmentCategoryEnum.DMR.getParticipantEnrollmentCategory()), - scrnaParticipantRepository.getParticipantCount(), - scrnaParticipantRepository.getParticipantCount())); - dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), - FullDataTypeEnum.SINGLE_NUCLEUS.getFullName(), FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(), - snrnaGeneExpressionRepository.getCountByEnrollment(EnrollmentCategoryEnum.AKI.getParticipantEnrollmentCategory()), - snrnaGeneExpressionRepository.getCountByEnrollment(EnrollmentCategoryEnum.CKD.getParticipantEnrollmentCategory()), - snrnaGeneExpressionRepository - .getCountByEnrollment(EnrollmentCategoryEnum.HEALTHY_REFERENCE.getParticipantEnrollmentCategory()), - snrnaGeneExpressionRepository.getCountByEnrollment(EnrollmentCategoryEnum.DMR.getParticipantEnrollmentCategory()), - snrnaParticipantRepository.getParticipantCount(), - snrnaParticipantRepository.getParticipantCount())); - dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), - FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getFullName(), - FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation(), - rtParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.AKI.getParticipantEnrollmentCategory()), - rtParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.CKD.getParticipantEnrollmentCategory()), - rtParticipantRepository - .getCountByEnrollmentCategory(EnrollmentCategoryEnum.HEALTHY_REFERENCE.getParticipantEnrollmentCategory()), - rtParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.DMR.getParticipantEnrollmentCategory()), - rtParticipantRepository.getParticipantCount(), - rtParticipantRepository.getParticipantCount())); - dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), - FullDataTypeEnum.REGIONAL_PROTEOMICS.getFullName(), - FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation(), - rpParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.AKI.getParticipantEnrollmentCategory()), - rpParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.CKD.getParticipantEnrollmentCategory()), - rpParticipantRepository - .getCountByEnrollmentCategory(EnrollmentCategoryEnum.HEALTHY_REFERENCE.getParticipantEnrollmentCategory()), - rpParticipantRepository.getCountByEnrollmentCategory(EnrollmentCategoryEnum.DMR.getParticipantEnrollmentCategory()), - rpParticipantRepository.getParticipantCount(), - rpParticipantRepository.getParticipantCount())); - return dataTypeSummary; - } - -} \ No newline at end of file diff --git a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService2025.java index 967578ae..e4a86f03 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; } diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java deleted file mode 100755 index 6ac88b9d..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionExpressionSummaryValue.java +++ /dev/null @@ -1,206 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleCell; - -import java.beans.Transient; -import java.io.Serializable; - -import jakarta.annotation.Nullable; -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.IdClass; -import jakarta.persistence.Table; - -import org.apache.commons.lang3.builder.EqualsBuilder; -import org.apache.commons.lang3.builder.HashCodeBuilder; -import org.kpmp.FullDataTypeEnum; -import org.kpmp.geneExpressionSummary.GeneExpressionId; -import org.kpmp.geneExpressionSummary.GeneExpressionSummary; - -@Entity -@Table(name = "sc_rnaseq") -@IdClass(GeneExpressionId.class) -public class SCRNAGeneExpressionExpressionSummaryValue implements GeneExpressionSummary, Serializable { - - private static final long serialVersionUID = 7265280085624504185L; - @Column(name = "id") - private Integer id; - @Column(name = "enrollment_category") - private String enrollmentCategory; - @Id - @Column(name = "gene") - private String gene; - @Column(name = "p_val") - private Double pVal; - @Column(name = "p_val_adj") - private Double pValAdj; - @Column(name = "fold_change") - private Double foldChange; - @Column(name = "pct_1") - private Double pct1; - @Column(name = "pct_2") - private Double pct2; - @Column(name = "avg_exp") - private Double avgExp; - @Id - @Column(name = "cluster") - private String cluster; - - @Column(name = "cluster_name") - private String clusterName; - - @Column(name = "cell_count") - private Integer cellCount; - - @Override - @Transient - public String getDataType() { - return FullDataTypeEnum.SINGLE_CELL.getAbbreviation(); - } - - @Override - public void setCellCount(Integer cellCount) { - this.cellCount = cellCount; - } - - @Override - public Integer getCellCount() { - return this.cellCount; - } - - @Override - public void setClusterName(String clusterName) { - this.clusterName = clusterName; - } - - @Nullable - @Override - public String getClusterName() { - return this.clusterName; - } - - @Override - @Nullable - public Integer getId() { - return id; - } - - @Override - public void setId(Integer id) { - this.id = id; - } - - @Override - @Nullable - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - @Override - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } - - @Override - @Nullable - public String getGene() { - return gene; - } - - @Override - public void setGene(String gene) { - this.gene = gene; - } - - @Override - @Nullable - public Double getPVal() { - return pVal; - } - - @Override - public void setPVal(Double pVal) { - this.pVal = pVal; - } - - @Override - @Nullable - public Double getPValAdj() { - return pValAdj; - } - - @Override - public void setPValAdj(Double pValAdj) { - this.pValAdj = pValAdj; - } - - @Override - @Nullable - public Double getFoldChange() { - return foldChange; - } - - @Override - public void setFoldChange(Double foldChange) { - this.foldChange = foldChange; - } - - @Override - @Nullable - public Double getPct1() { - return pct1; - } - - @Override - public void setPct1(Double pct1) { - this.pct1 = pct1; - } - - @Override - @Nullable - public Double getPct2() { - return pct2; - } - - @Override - public void setPct2(Double pct2) { - this.pct2 = pct2; - } - - @Override - @Nullable - public Double getAvgExp() { - return avgExp; - } - - @Override - public void setAvgExp(Double avgExp) { - this.avgExp = avgExp; - } - - @Override - @Nullable - public String getCluster() { - return cluster; - } - - @Override - public void setCluster(String cluster) { - this.cluster = cluster; - } - - @Override - public int hashCode() { - return new HashCodeBuilder().append(gene).append(cluster).build(); - } - - @Override - public boolean equals(Object obj) { - if (obj == this) - return true; - if (!(obj instanceof SCRNAGeneExpressionExpressionSummaryValue)) - return false; - SCRNAGeneExpressionExpressionSummaryValue that = (SCRNAGeneExpressionExpressionSummaryValue) obj; - return new EqualsBuilder().append(this.gene, that.gene).append(this.cluster, that.cluster).build(); - } - -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionSummaryRepository.java b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionSummaryRepository.java deleted file mode 100755 index 57db52fc..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAGeneExpressionSummaryRepository.java +++ /dev/null @@ -1,40 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleCell; - -import java.util.List; - -import org.kpmp.geneExpressionSummary.GeneExpressionId; -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.data.repository.query.Param; -import org.springframework.stereotype.Repository; - -@Repository -public interface SCRNAGeneExpressionSummaryRepository - extends CrudRepository { - - @Cacheable("scCountsAllClusters") - @Query(value = "SELECT DISTINCT scc.cluster, scc.cluster_name, scc.cell_count, scc.cluster_id as id, IF(isnull(scr.enrollment_category), :enrollmentCategory, scr.enrollment_category) as enrollment_category, IF(isnull(scr.gene), :geneSymbol, scr.gene) as gene, scr.p_val as p_val, scr.p_val_adj as p_val_adj, scr.fold_change, scr.pct_1, scr.pct_2, scr.avg_exp as avg_exp " - + "FROM sc_cluster_v scc " - + "LEFT JOIN sc_rnaseq scr ON scc.cluster = scr.cluster AND scr.gene = :geneSymbol AND scr.enrollment_category = LCASE(:enrollmentCategory) " - + "WHERE scc.enrollment_category = LCASE(:enrollmentCategory) ORDER BY scr.p_val IS NULL, scr.p_val ASC", nativeQuery = true) - List findByEnrollmentAndGeneAllClusters( - @Param("geneSymbol") String geneSymbol, @Param("enrollmentCategory") String enrollmentCategory); - - @Cacheable("scCountsSummaryPerGene") - @Query(value = "SELECT DISTINCT scr.cluster, c.cluster_name, 0 as cell_count, scr.id, scr.enrollment_category, scr.gene, scr.p_val as p_val, scr.p_val_adj as p_val_adj, scr.fold_change, scr.pct_1, scr.pct_2, scr.avg_exp as avg_exp " - + "FROM sc_rnaseq scr " + "JOIN cluster c ON scr.cluster = c.abbreviation AND c.cluster_name = :cellType " - + "WHERE scr.enrollment_category = LCASE(:enrollmentCategory) " + "ORDER BY scr.fold_change DESC", nativeQuery = true) - List findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory( - @Param("cellType") String cellType, @Param("enrollmentCategory") String enrollmentCategory); - - @Cacheable("scCountsByGene") - @Query(value = "SELECT COUNT(*) FROM sc_rnaseq scr WHERE scr.gene= :gene", nativeQuery = true) - long getCountByGene(@Param("gene") String gene); - - @Cacheable("scCountsByEnrollment") - @Query(value = "select count(*) from (select p.redcap_id from sc_metadata sc " - + "join participant p on sc.specimen_id = p.redcap_id " - + "where p.enrollment_category=:enrollmentCategory group by p.redcap_id) as mycount", nativeQuery = true) - long getCountByEnrollment(@Param("enrollmentCategory") String enrollmentCategory); -} \ No newline at end of file diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantRepository.java b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantRepository.java deleted file mode 100755 index 26b8933f..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantRepository.java +++ /dev/null @@ -1,14 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleCell; - -import org.kpmp.geneExpressionSummary.ParticipantId; -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.stereotype.Repository; - -@Repository -public interface SCRNAParticipantRepository extends CrudRepository { - @Cacheable("scParticipantCount") - @Query(value = "SELECT COUNT(DISTINCT scp.redcap_id) FROM sc_participant_tissue_v scp", nativeQuery = true) - Long getParticipantCount(); -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java deleted file mode 100755 index 6db627b2..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleCell/SCRNAParticipantValue.java +++ /dev/null @@ -1,42 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleCell; - -import org.kpmp.geneExpressionSummary.ParticipantId; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.IdClass; -import jakarta.persistence.Table; - -@Entity -@Table(name = "sn_participant_tissue_v") -@IdClass(ParticipantId.class) -public class SCRNAParticipantValue implements Serializable { - - private static final long serialVersionUID = 8746341469788157316L; - - @Column(name = "enrollment_category") - private String enrollmentCategory; - - @Column(name = "redcap_id") - private String redcapId; - - @Id - public String getRedcapId() { - return redcapId; - } - - public void setRedcapId(String redcapId) { - this.redcapId = redcapId; - } - - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java deleted file mode 100755 index 22cd94d3..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionExpressionSummaryValue.java +++ /dev/null @@ -1,218 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleNucleus; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.IdClass; -import jakarta.persistence.Table; -import jakarta.persistence.Transient; - -import org.kpmp.FullDataTypeEnum; -import org.kpmp.geneExpressionSummary.GeneExpressionId; -import org.kpmp.geneExpressionSummary.GeneExpressionSummary; -import org.springframework.lang.Nullable; - -@Entity -@Table(name = "sn_rnaseq") -@IdClass(GeneExpressionId.class) -public class SNRNAGeneExpressionExpressionSummaryValue implements GeneExpressionSummary, Serializable { - - private static final long serialVersionUID = -443713903175981503L; - - @Column(name = "id") - private Integer id; - - @Column(name = "enrollment_category") - private String enrollmentCategory; - - @Id - @Column(name = "gene") - private String gene; - - @Column(name = "p_val") - private Double pVal; - - @Column(name = "p_val_adj") - private Double pValAdj; - - @Column(name = "fold_change") - private Double foldChange; - - @Column(name = "pct_1") - private Double pct1; - - @Column(name = "pct_2") - private Double pct2; - - @Column(name = "avg_exp") - private Double avgExp; - - @Id - @Column(name = "cluster") - private String cluster; - - @Column(name = "cell_type") - private String cellType; - - @Override - @Transient - public String getDataType() { - return FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(); - } - - @Column(name = "cluster_name") - private String clusterName; - - @Column(name = "cell_count") - private Integer cellCount; - - @Override - @Nullable - public Integer getId() { - return id; - } - - @Override - public void setId(Integer id) { - this.id = id; - } - - @Override - @Nullable - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - @Override - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } - - @Override - @Nullable - public String getGene() { - return gene; - } - - @Override - public void setGene(String gene) { - this.gene = gene; - } - - @Override - @Nullable - public Double getPVal() { - return pVal; - } - - @Override - public void setPVal(Double pVal) { - this.pVal = pVal; - } - - @Override - @Nullable - public Double getPValAdj() { - return pValAdj; - } - - @Override - public void setPValAdj(Double pValAdj) { - this.pValAdj = pValAdj; - } - - @Override - @Nullable - public Double getFoldChange() { - return foldChange; - } - - @Override - public void setFoldChange(Double foldChange) { - this.foldChange = foldChange; - } - - @Override - @Nullable - public Double getPct1() { - return pct1; - } - - @Override - public void setPct1(Double pct1) { - this.pct1 = pct1; - } - - @Override - @Nullable - public Double getPct2() { - return pct2; - } - - @Override - public void setPct2(Double pct2) { - this.pct2 = pct2; - } - - @Override - @Nullable - public Double getAvgExp() { - return avgExp; - } - - @Override - @Nullable - public void setAvgExp(Double avgExp) { - this.avgExp = avgExp; - } - - @Id - @Override - public String getCluster() { - return cluster; - } - - @Override - public void setCluster(String cluster) { - this.cluster = cluster; - } - - @Override - public void setCellCount(Integer cellCount) { - this.cellCount = cellCount; - } - - @Override - public Integer getCellCount() { - return this.cellCount; - } - - @Override - public void setClusterName(String clusterName) { - this.clusterName = clusterName; - } - - @Nullable - @Override - public String getClusterName() { - return this.clusterName; - } - - @Override - public int hashCode() { - return (gene + cluster).hashCode(); - } - - @Override - public boolean equals(Object obj) { - if (obj == this) - return true; - if (!(obj instanceof SNRNAGeneExpressionExpressionSummaryValue)) - return false; - SNRNAGeneExpressionExpressionSummaryValue snrnaGeneExpressionExpressionSummaryValue = (SNRNAGeneExpressionExpressionSummaryValue) obj; - return (snrnaGeneExpressionExpressionSummaryValue.getGene().equals(this.getGene()) - && snrnaGeneExpressionExpressionSummaryValue.getCluster().equals(this.getCluster())); - } -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionSummaryRepository.java b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionSummaryRepository.java deleted file mode 100755 index 66bbc84c..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAGeneExpressionSummaryRepository.java +++ /dev/null @@ -1,40 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleNucleus; - -import java.util.List; - -import org.kpmp.geneExpressionSummary.GeneExpressionId; -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.data.repository.query.Param; -import org.springframework.stereotype.Repository; - -@Repository -public interface SNRNAGeneExpressionSummaryRepository - extends CrudRepository { - - @Cacheable("snCountsBy") - @Query(value = "SELECT DISTINCT snc.cluster, snc.cluster_name, snc.cell_count as cell_count, snc.cluster_id as id, IF(isnull(snr.enrollment_category), :enrollmentCategory, snr.enrollment_category) as enrollment_category, IF(isnull(snr.gene), :geneSymbol, snr.gene) as gene, snr.p_val as pval, snr.p_val_adj as pval_adj, snr.fold_change, snr.pct_1 as pct1, snr.pct_2 as pct2, snr.avg_exp as avg_exp " - + "FROM sn_cluster_v snc " - + "LEFT JOIN sn_rnaseq snr ON snc.cluster = snr.cluster AND snr.gene = :geneSymbol AND snr.enrollment_category = LCASE(:enrollmentCategory) " - + "WHERE snc.enrollment_category = LCASE(:enrollmentCategory) ORDER BY snr.p_val IS NULL, snr.p_val ASC", nativeQuery = true) - List findByEnrollmentAndGeneAllClusters( - @Param("geneSymbol") String geneSymbol, @Param("enrollmentCategory") String enrollmentCategory); - - @Cacheable("snCounts") - @Query(value = "SELECT DISTINCT snr.cluster, c.cluster_name, 0 as cell_count, snr.id, snr.enrollment_category, snr.gene, snr.p_val as pval, snr.p_val_adj as pval_adj, snr.fold_change, snr.pct_1 as pct1, snr.pct_2 as pct2, snr.avg_exp as avg_exp " - + "FROM sn_rnaseq snr " + "JOIN cluster c ON snr.cluster = c.abbreviation AND c.cluster_name = :cellType " - + "WHERE snr.enrollment_category = LCASE(:enrollmentCategory) " + "ORDER BY snr.fold_change DESC", nativeQuery = true) - List findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory( - @Param("cellType") String cellType, @Param("enrollmentCategory") String enrollmentCategory); - - @Cacheable("snCounts") - @Query(value = "select count(*) from (select p.redcap_id from sn_metadata sn " - + "join participant p on sn.specimen_id = p.redcap_id " - + "where p.enrollment_category=:enrollmentCategory group by p.redcap_id) as mycount", nativeQuery = true) - long getCountByEnrollment(@Param("enrollmentCategory") String enrollmentCategory); - - @Cacheable("snCounts") - @Query(value = "SELECT COUNT(*) FROM sn_rnaseq snr WHERE snr.gene= :gene", nativeQuery = true) - long getCountByGene(@Param("gene") String gene); -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantRepository.java b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantRepository.java deleted file mode 100755 index c2e146ba..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantRepository.java +++ /dev/null @@ -1,15 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleNucleus; - -import org.kpmp.geneExpressionSummary.ParticipantId; -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.stereotype.Repository; - -@Repository -public interface SNRNAParticipantRepository extends CrudRepository { - - @Cacheable("snParticipantCount") - @Query(value = "SELECT COUNT(DISTINCT snp.redcap_id) FROM sn_participant_tissue_v snp", nativeQuery = true) - Long getParticipantCount(); -} diff --git a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java deleted file mode 100755 index a478ebdf..00000000 --- a/src/main/java/org/kpmp/geneExpressionSummary/singleNucleus/SNRNAParticipantValue.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.kpmp.geneExpressionSummary.singleNucleus; - -import org.kpmp.geneExpressionSummary.Participant; -import org.kpmp.geneExpressionSummary.ParticipantId; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.IdClass; -import jakarta.persistence.Table; - -@Entity -@Table(name = "sn_participant_tissue_v") -@IdClass(ParticipantId.class) -public class SNRNAParticipantValue implements Participant, Serializable { - - private static final long serialVersionUID = -2404700991479961255L; - - @Column(name = "enrollment_category") - private String enrollmentCategory; - - @Column(name = "redcap_id") - private String redcapId; - - @Override - @Id - public String getRedcapId() { - return redcapId; - } - - @Override - public void setRedcapId(String redcapId) { - this.redcapId = redcapId; - } - - @Override - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - @Override - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } -} diff --git a/src/main/java/org/kpmp/participant/ParticipantDataTypeInformation.java b/src/main/java/org/kpmp/participant/ParticipantDataTypeInformation.java deleted file mode 100755 index 20eab4a9..00000000 --- a/src/main/java/org/kpmp/participant/ParticipantDataTypeInformation.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.kpmp.participant; - -import org.springframework.stereotype.Component; - -@Component -public class ParticipantDataTypeInformation { - - private String dataType; - private Integer count; - private Boolean isAggregatedData; - - public ParticipantDataTypeInformation() { - // default constructor so spring does not complain - } - - public ParticipantDataTypeInformation(String dataType, Integer count, boolean isAggregatedData) { - this.dataType = dataType; - this.count = count; - this.isAggregatedData = isAggregatedData; - - } - - public String getDataType() { - return dataType; - } - - public void setDataType(String dataType) { - this.dataType = dataType; - } - - public Integer getCount() { - return count; - } - - public void setCount(Integer count) { - this.count = count; - } - - public boolean isAggregatedData() { - return isAggregatedData; - } - - public void setAggregatedData(boolean isAggregatedData) { - this.isAggregatedData = isAggregatedData; - } - -} diff --git a/src/main/java/org/kpmp/participant/ParticipantDataTypeSummary.java b/src/main/java/org/kpmp/participant/ParticipantDataTypeSummary.java deleted file mode 100755 index a3c33835..00000000 --- a/src/main/java/org/kpmp/participant/ParticipantDataTypeSummary.java +++ /dev/null @@ -1,27 +0,0 @@ -package org.kpmp.participant; - -import java.util.List; - -import org.springframework.stereotype.Component; - -@Component -public class ParticipantDataTypeSummary { - private List spatialViewerDataTypes; - private List explorerDataTypes; - - public List getSpatialViewerDataTypes() { - return spatialViewerDataTypes; - } - - public void setSpatialViewerDataTypes(List spatialViewerDataTypes) { - this.spatialViewerDataTypes = spatialViewerDataTypes; - } - - public List getExplorerDataTypes() { - return explorerDataTypes; - } - - public void setExplorerDataTypes(List explorerDataTypes) { - this.explorerDataTypes = explorerDataTypes; - } -} diff --git a/src/main/java/org/kpmp/participant/ParticipantService.java b/src/main/java/org/kpmp/participant/ParticipantService.java deleted file mode 100755 index ef53b3e7..00000000 --- a/src/main/java/org/kpmp/participant/ParticipantService.java +++ /dev/null @@ -1,224 +0,0 @@ -package org.kpmp.participant; - -import java.util.ArrayList; -import java.util.Collection; -import java.util.Comparator; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.kpmp.FullDataTypeEnum; -import org.kpmp.EnrollmentCategoryEnum; -import org.kpmp.dataSummary.AtlasRepositoryLinkInformation; -import org.kpmp.dataSummary.DataSummaryRepository; -import org.kpmp.geneExpressionSummary.regionalProteomics.RPParticipantRepository; -import org.kpmp.geneExpressionSummary.regionalTranscriptomics.RTParticipantRepository; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.beans.factory.annotation.Value; -import org.springframework.stereotype.Service; - -@Service -public class ParticipantService { - @Value("${experiment.label.clinicalStudyData}") - private String CLINICAL_STUDY_DATA; - @Value("${experiment.label.biomarkers}") - private String BIOMARKERS; - @Value("${experiment.category.biomarker}") - private String BIOMARKER; - - - private ParticipantSummaryDatasetRepository participantSummaryDatasetRepository; - private DataSummaryRepository dataSummaryRepo; - private SpatialViewerTypeRepository svTypeRepo; - private SingleCellMetadataRepository scMetadataRepo; - private Logger logger = LoggerFactory.getLogger(ParticipantService.class); - - private final String SPATIAL_VIEWER_FILE_VIEW = "sv_file_v"; - private final String SPATIAL_VIEWER_LINK_VIEW = "sv_link_v"; - private SingleNucleusMetadataRepository snMetadataRepo; - private SingleNucleusMetadataRepository2025 snMetadataRepo2025; - private RTParticipantRepository rtParticipantRepo; - private ParticipantRepoDataRepository fileByParticipantRepo; - private RPParticipantRepository rpParticipantRepository; - private ParticipantClinicalDatasetRepository participantClinicalDatasetRepo; - - @Autowired - public ParticipantService(DataSummaryRepository dataSummaryRepo, SpatialViewerTypeRepository svTypeRepo, - SingleCellMetadataRepository scMetadataRepo, SingleNucleusMetadataRepository snMetadataRepo, - SingleNucleusMetadataRepository2025 snMetadataRepo2025, - RTParticipantRepository rtParticipantRepo, - ParticipantSummaryDatasetRepository participantSummaryDatasetRepository, RPParticipantRepository rpParticipantRepository, - ParticipantRepoDataRepository fileByParticipantRepo, ParticipantClinicalDatasetRepository participantClinicalDatasetRepo) { - this.dataSummaryRepo = dataSummaryRepo; - this.svTypeRepo = svTypeRepo; - this.scMetadataRepo = scMetadataRepo; - this.snMetadataRepo = snMetadataRepo; - this.rtParticipantRepo = rtParticipantRepo; - this.participantSummaryDatasetRepository = participantSummaryDatasetRepository; - this.rpParticipantRepository = rpParticipantRepository; - this.fileByParticipantRepo = fileByParticipantRepo; - this.participantClinicalDatasetRepo = participantClinicalDatasetRepo; - this.snMetadataRepo2025 = snMetadataRepo2025; - } - - public ParticipantClinicalDataset getParticipantClinicalDataset(String redcapId){ - Integer participantId = participantSummaryDatasetRepository.findIdByRedcapId(redcapId); - return participantClinicalDatasetRepo.findByParticipantId(participantId); - } - - public ParticipantSummaryDataset getParticipantSummaryDataset(String redcapId) { - return participantSummaryDatasetRepository.findByRedcapId(redcapId); - } - - public List getEnrollmentData() { - List enrollmentData = new ArrayList<>(); - - enrollmentData.add(new ParticipantEnrollmentCategorySummary( - participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.AKI.getParticipantEnrollmentCategory()), - participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.CKD.getParticipantEnrollmentCategory()), - participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.HEALTHY_REFERENCE.getParticipantEnrollmentCategory()), - participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.DMR.getParticipantEnrollmentCategory()))); - return enrollmentData; - } - - public ParticipantRepoDataTypeSummary getDataTypeCounts(String redcapId) { - ParticipantRepoDataTypeSummary summaryData = new ParticipantRepoDataTypeSummary(); - summaryData.setRepositoryDataTypes(getRepositoryCounts(redcapId)); - return summaryData; - } - - public ParticipantDataTypeSummary getExperimentCounts(String redcapId) { - ParticipantDataTypeSummary summaryData = new ParticipantDataTypeSummary(); - summaryData.setSpatialViewerDataTypes(getSpatialViewerCounts(redcapId)); - summaryData.setExplorerDataTypes(getExplorerCounts(redcapId)); - - return summaryData; - } - - public ParticipantRepoDataTypeInformation getTotalFilesCount(String redcapId) { - String participant_id = dataSummaryRepo.getParticipantIDString(redcapId); - Integer totalCount = dataSummaryRepo.getParticipantTotalFileCount(participant_id); - AtlasRepositoryLinkInformation linkInfo = new AtlasRepositoryLinkInformation("redcap_id", redcapId); - ParticipantRepoDataTypeInformation res = new ParticipantRepoDataTypeInformation("", totalCount, linkInfo); - - return res; - } - - public List getExperimentalStrategyCountsByParticipant(String redcapId) { - // this behaves in much the same way as DataSummaryService.getAtlasRepoSummary does to coallate link types together - // But, the underlying object structure was different enough I couldn't figure out a way to merge them into one implemention - - List fileCountsForParticipant = fileByParticipantRepo.findFileCountsByParticipant(redcapId); - Map resultMap = new HashMap<>(); - - for (ParticipantRepoData participantRepoData : fileCountsForParticipant) { - String experimentalStrategy = participantRepoData.getExperimentalStrategy(); - AtlasRepositoryLinkInformation linkInfo = new AtlasRepositoryLinkInformation(AtlasRepositoryLinkInformation.EXPERIMENTAL_STRATEGY, experimentalStrategy); - if (experimentalStrategy.isEmpty() && participantRepoData.getDataType().equalsIgnoreCase(CLINICAL_STUDY_DATA)) { - experimentalStrategy = CLINICAL_STUDY_DATA; - linkInfo = new AtlasRepositoryLinkInformation(AtlasRepositoryLinkInformation.DATA_CATEGORY, participantRepoData.getDataCategory()); - } else if (participantRepoData.getDataCategory().equalsIgnoreCase(BIOMARKER)) { - experimentalStrategy = BIOMARKERS; - linkInfo = new AtlasRepositoryLinkInformation(AtlasRepositoryLinkInformation.DATA_CATEGORY, participantRepoData.getDataCategory()); - } - - if (resultMap.containsKey(experimentalStrategy)) { - ParticipantRepoDataTypeInformation existingRecord = resultMap.get(experimentalStrategy); - existingRecord.setCount(existingRecord.getCount() + participantRepoData.getCount()); - } else { - - ParticipantRepoDataTypeInformation dataInformation = new ParticipantRepoDataTypeInformation(experimentalStrategy, participantRepoData.getCount(), linkInfo); - - resultMap.put(experimentalStrategy, dataInformation); - } - - } - - Collection values = resultMap.values(); - List results = new ArrayList<>(values); - results.sort(new Comparator() { - public int compare(ParticipantRepoDataTypeInformation one, ParticipantRepoDataTypeInformation two) { - return one.getDataType().compareToIgnoreCase(two.getDataType()); - } - }); - - return results; - } - - private List getExplorerCounts(String redcapId) { - List explorerExperiments = new ArrayList<>(); - int scCount = 0; - if (scMetadataRepo.existsByRedcapId(redcapId)) { - scCount = 1; - } - - ParticipantDataTypeInformation singleCellData = new ParticipantDataTypeInformation( - FullDataTypeEnum.SINGLE_CELL.getFullName(), scCount, true); - explorerExperiments.add(singleCellData); - - int snCount = 0; - if (snMetadataRepo.existsByRedcapId(redcapId)) { - snCount = 1; - } - ParticipantDataTypeInformation singleNucData = new ParticipantDataTypeInformation( - FullDataTypeEnum.SINGLE_NUCLEUS.getFullName(), snCount, true); - explorerExperiments.add(singleNucData); - - int regionalTranscriptomicsCount = 0; - if (rtParticipantRepo.existsByRedcapId(redcapId)) { - regionalTranscriptomicsCount = 1; - } - ParticipantDataTypeInformation regionalTranscriptomicsData = new ParticipantDataTypeInformation( - FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getFullName(), regionalTranscriptomicsCount, true); - explorerExperiments.add(regionalTranscriptomicsData); - - int regionalProteomicsCount = 0; - if (rpParticipantRepository.existsByRedcapId(redcapId)) { - regionalProteomicsCount = 1; - } - ParticipantDataTypeInformation regionalProteomicsData = new ParticipantDataTypeInformation( - FullDataTypeEnum.REGIONAL_PROTEOMICS.getFullName(), regionalProteomicsCount, true); - explorerExperiments.add(regionalProteomicsData); - - return explorerExperiments; - } - - private List getSpatialViewerCounts(String redcapId) { - List spatialViewerExperiments = new ArrayList<>(); - - List spatialViewerDataTypes = svTypeRepo.findAll(); - for (SpatialViewerDataType spatialViewerDataType : spatialViewerDataTypes) { - String dataType = spatialViewerDataType.getDataType(); - if (spatialViewerDataType.getTableName().equals(SPATIAL_VIEWER_FILE_VIEW)) { - - Integer count = dataSummaryRepo.getParticipantSvFileDataTypeCount(redcapId, dataType); - ParticipantDataTypeInformation dataTypeInfo = new ParticipantDataTypeInformation(dataType, count, - false); - spatialViewerExperiments.add(dataTypeInfo); - } else if (spatialViewerDataType.getTableName().equals(SPATIAL_VIEWER_LINK_VIEW)) { - Integer count = dataSummaryRepo.getParticipantSvLinkDataTypeCount(redcapId, dataType); - ParticipantDataTypeInformation dataTypeInfo = new ParticipantDataTypeInformation(dataType, count, - false); - spatialViewerExperiments.add(dataTypeInfo); - } else { - logger.error("Unable to query for data type: " + dataType + ". Need to change code to handle."); - } - } - return spatialViewerExperiments; - } - - private List getRepositoryCounts(String redcapId) { - List repoCounts = new ArrayList<>(); - - List repoDataTypes = dataSummaryRepo.getRepoDataTypes(); - for (String repoDataType : repoDataTypes) { - Integer count = dataSummaryRepo.getParticipantRepoFileDataTypeCount(redcapId, repoDataType); - AtlasRepositoryLinkInformation linkInformation = new AtlasRepositoryLinkInformation("data_type", repoDataType); - ParticipantRepoDataTypeInformation dataTypeInfo = new ParticipantRepoDataTypeInformation(repoDataType, count, linkInformation); - repoCounts.add(dataTypeInfo); - } - return repoCounts; - } -} \ No newline at end of file diff --git a/src/main/java/org/kpmp/participant/ParticipantService2025.java b/src/main/java/org/kpmp/participant/ParticipantService2025.java index 733b3364..ca3dd516 100755 --- a/src/main/java/org/kpmp/participant/ParticipantService2025.java +++ b/src/main/java/org/kpmp/participant/ParticipantService2025.java @@ -33,7 +33,7 @@ public class ParticipantService2025 { private DataSummaryRepository dataSummaryRepo; private SpatialViewerTypeRepository svTypeRepo; private SingleCellMetadataRepository2025 scMetadataRepo2025; - private Logger logger = LoggerFactory.getLogger(ParticipantService.class); + private Logger logger = LoggerFactory.getLogger(ParticipantService2025.class); private final String SPATIAL_VIEWER_FILE_VIEW = "sv_file_v"; private final String SPATIAL_VIEWER_LINK_VIEW = "sv_link_v"; diff --git a/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java b/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java deleted file mode 100755 index 4b151c6f..00000000 --- a/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java +++ /dev/null @@ -1,36 +0,0 @@ -package org.kpmp.participant; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.Table; - -@Entity -@Table(name = "sn_metadata") -class SingleNucleusMetadata implements Serializable { - - private static final long serialVersionUID = -504357775835334661L; - @Id - private String barcode; - @Column(name = "specimen_id") - private String redcapId; - - public String getBarcode() { - return barcode; - } - - public void setBarcode(String barcode) { - this.barcode = barcode; - } - - public String getRedcapId() { - return redcapId; - } - - public void setRedcapId(String redcapId) { - this.redcapId = redcapId; - } - -} diff --git a/src/main/java/org/kpmp/participant/SingleNucleusMetadataRepository.java b/src/main/java/org/kpmp/participant/SingleNucleusMetadataRepository.java deleted file mode 100755 index fbaad996..00000000 --- a/src/main/java/org/kpmp/participant/SingleNucleusMetadataRepository.java +++ /dev/null @@ -1,12 +0,0 @@ -package org.kpmp.participant; - -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.repository.CrudRepository; - -public interface SingleNucleusMetadataRepository extends CrudRepository { - - @Cacheable("snParticipantExistsByRedcap") - - boolean existsByRedcapId(String redcapId); - -} diff --git a/src/main/java/org/kpmp/umap/SCMetadata.java b/src/main/java/org/kpmp/umap/SCMetadata.java deleted file mode 100755 index 9509b5ea..00000000 --- a/src/main/java/org/kpmp/umap/SCMetadata.java +++ /dev/null @@ -1,112 +0,0 @@ -package org.kpmp.umap; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.Table; -import jakarta.persistence.Transient; - -@Entity -@Table(name = "sc_umap_point_v") -public class SCMetadata implements UmapPoint, Serializable { - - private static final long serialVersionUID = 7947867645080936879L; - @Column(name = "umap_x") - private double umapX; - @Column(name = "umap_y") - private double umapY; - @Column(name = "cluster_abbreviation") - private String clusterAbbreviation; - @Column(name = "cluster_name") - private String clusterName; - @Column(name = "cluster_color") - private String clusterColor; - @Id - @Column(name = "barcode") - private String barcode; - @Column(name = "enrollment_category") - private String enrollmentCategory; - @Transient - private double expressionValue; - - @Override - public double getUmapX() { - return umapX; - } - - @Override - public void setUmapX(double umapX) { - this.umapX = umapX; - } - - @Override - public double getUmapY() { - return umapY; - } - - @Override - public void setUmapY(double umapY) { - this.umapY = umapY; - } - - @Override - public String getClusterName() { - return clusterName; - } - - @Override - public void setClusterName(String clusterName) { - this.clusterName = clusterName; - } - - @Override - public String getClusterAbbreviation() { - return clusterAbbreviation; - } - - @Override - public void setClusterAbbreviation(String clusterAbbreviation) { - this.clusterAbbreviation = clusterAbbreviation; - } - - @Override - public String getClusterColor() { - return clusterColor; - } - - @Override - public void setClusterColor(String clusterColor) { - this.clusterColor = clusterColor; - } - - @Override - public double getExpressionValue() { - return this.expressionValue; - } - - @Override - public void setExpressionValue(double expressionValue) { - this.expressionValue = expressionValue; - } - - @Override - public String getBarcode() { - return this.barcode; - } - - @Override - public void setBarcode(String barcode) { - this.barcode = barcode; - } - - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } - -} diff --git a/src/main/java/org/kpmp/umap/SCMetadataRepository.java b/src/main/java/org/kpmp/umap/SCMetadataRepository.java deleted file mode 100755 index 7b508e39..00000000 --- a/src/main/java/org/kpmp/umap/SCMetadataRepository.java +++ /dev/null @@ -1,50 +0,0 @@ -package org.kpmp.umap; - -import java.util.List; - -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.data.repository.query.Param; - -public interface SCMetadataRepository extends CrudRepository { - - @Cacheable("scMetadataAll") - @Override - List findAll(); - - @Cacheable("scMetadataLimited") - @Query(value = "SELECT " - + "umap_x, " - + "umap_y, " - + "cluster_abbreviation, " - + "cluster_name, " - + "cluster_color, " - + "barcode, " - + "enrollment_category " - + "FROM sc_umap_point_v " - + "LIMIT :limit", nativeQuery = true) - List findLimited(@Param("limit") int limit); - - @Cacheable("scMetadataCount") - @Query(value = "SELECT COUNT(umap_x) FROM sc_umap_point_v;", nativeQuery = true) - int findCount(); - - List findByEnrollmentCategory(String enrollmentCategory); - - SCMetadata findByBarcode(String barcode); - - @Cacheable("scMetadataWithEnrollment") - @Query(value = "SELECT " - + "umap_x, " - + "umap_y, " - + "cluster_abbreviation, " - + "cluster_name, " - + "cluster_color, " - + "barcode, " - + "enrollment_category " - + "FROM sc_umap_point_v " - + "WHERE enrollment_category=:enrollmentCategory " - + "LIMIT :limit", nativeQuery = true) - List findLimitedWithEnrollmentCategory(@Param("enrollmentCategory") String enrollmentCategory, @Param("limit") int limit); -} diff --git a/src/main/java/org/kpmp/umap/SNMetadata.java b/src/main/java/org/kpmp/umap/SNMetadata.java deleted file mode 100755 index 6173c4eb..00000000 --- a/src/main/java/org/kpmp/umap/SNMetadata.java +++ /dev/null @@ -1,112 +0,0 @@ -package org.kpmp.umap; - -import java.io.Serializable; - -import jakarta.persistence.Column; -import jakarta.persistence.Entity; -import jakarta.persistence.Id; -import jakarta.persistence.Table; -import jakarta.persistence.Transient; - -@Entity -@Table(name = "sn_umap_point_v") -public class SNMetadata implements UmapPoint, Serializable { - - private static final long serialVersionUID = -8871186152958713643L; - @Column(name = "umap_x") - private double umapX; - @Column(name = "umap_y") - private double umapY; - @Column(name = "cluster_abbreviation") - private String clusterAbbreviation; - @Column(name = "cluster_name") - private String clusterName; - @Column(name = "cluster_color") - private String clusterColor; - @Id - @Column(name = "barcode") - private String barcode; - @Column(name = "enrollment_category") - private String enrollmentCategory; - @Transient - private double expressionValue; - - @Override - public double getUmapX() { - return umapX; - } - - @Override - public void setUmapX(double umapX) { - this.umapX = umapX; - } - - @Override - public double getUmapY() { - return umapY; - } - - @Override - public void setUmapY(double umapY) { - this.umapY = umapY; - } - - @Override - public String getClusterName() { - return clusterName; - } - - @Override - public void setClusterName(String clusterName) { - this.clusterName = clusterName; - } - - @Override - public String getClusterAbbreviation() { - return clusterAbbreviation; - } - - @Override - public void setClusterAbbreviation(String clusterAbbreviation) { - this.clusterAbbreviation = clusterAbbreviation; - } - - @Override - public String getClusterColor() { - return clusterColor; - } - - @Override - public void setClusterColor(String clusterColor) { - this.clusterColor = clusterColor; - } - - @Override - public double getExpressionValue() { - return this.expressionValue; - } - - @Override - public void setExpressionValue(double expressionValue) { - this.expressionValue = expressionValue; - } - - @Override - public String getBarcode() { - return this.barcode; - } - - @Override - public void setBarcode(String barcode) { - this.barcode = barcode; - } - - public String getEnrollmentCategory() { - return enrollmentCategory; - } - - public void setEnrollmentCategory(String enrollmentCategory) { - this.enrollmentCategory = enrollmentCategory; - } - -} diff --git a/src/main/java/org/kpmp/umap/SNMetadataRepository.java b/src/main/java/org/kpmp/umap/SNMetadataRepository.java deleted file mode 100755 index 8af9d5a9..00000000 --- a/src/main/java/org/kpmp/umap/SNMetadataRepository.java +++ /dev/null @@ -1,49 +0,0 @@ -package org.kpmp.umap; - -import java.util.List; - -import org.springframework.cache.annotation.Cacheable; -import org.springframework.data.jpa.repository.Query; -import org.springframework.data.repository.CrudRepository; -import org.springframework.data.repository.query.Param; - -interface SNMetadataRepository extends CrudRepository { - - @Cacheable("snMetadataAll") - @Override - List findAll(); - - @Cacheable("snMetadataLimited") - @Query(value = "SELECT " - + "umap_x, " - + "umap_y, " - + "cluster_abbreviation, " - + "cluster_name, " - + "cluster_color, " - + "barcode, " - + "enrollment_category " - + "FROM sn_umap_point_v " - + "LIMIT :limit", nativeQuery = true) - List findLimited(@Param("limit") int limit); - - @Cacheable("snMetadataCount") - @Query(value = "SELECT COUNT(umap_x) FROM sn_umap_point_v;", nativeQuery = true) - int findCount(); - - @Cacheable("snMetadataByEnrollment") - List findByEnrollmentCategory(String enrollmentCategory); - - @Cacheable("snMetadataWithEnrollment") - @Query(value = "SELECT " - + "umap_x, " - + "umap_y, " - + "cluster_abbreviation, " - + "cluster_name, " - + "cluster_color, " - + "barcode, " - + "enrollment_category " - + "FROM sn_umap_point_v " - + "WHERE enrollment_category=:enrollmentCategory " - + "LIMIT :limit", nativeQuery = true) - List findLimitedWithEnrollmentCategory(@Param("enrollmentCategory") String enrollmentCategory, @Param("limit") int limit); -} diff --git a/src/main/java/org/kpmp/umap/SNMetadataRepository2025.java b/src/main/java/org/kpmp/umap/SNMetadataRepository2025.java index 14303b37..5054e1f2 100755 --- a/src/main/java/org/kpmp/umap/SNMetadataRepository2025.java +++ b/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; diff --git a/src/main/java/org/kpmp/umap/UmapDataService.java b/src/main/java/org/kpmp/umap/UmapDataService.java deleted file mode 100755 index 3e531dff..00000000 --- a/src/main/java/org/kpmp/umap/UmapDataService.java +++ /dev/null @@ -1,128 +0,0 @@ -package org.kpmp.umap; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Iterator; - -import org.json.JSONException; -import org.json.JSONObject; -import org.kpmp.EnrollmentCategoryEnum; -import org.kpmp.FullDataTypeEnum; -import org.kpmp.geneExpression.SNSCExpressionDataService; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.stereotype.Service; - -@Service -public class UmapDataService { - - private SNSCExpressionDataService expressionService; - private SNMetadataRepository snMetadataRepo; - private SCMetadataRepository scMetadataRepo; - - @Autowired - public UmapDataService(SCMetadataRepository scMetadataRepo, SNMetadataRepository snMetadataRepo, - SNSCExpressionDataService expressionService) { - this.scMetadataRepo = scMetadataRepo; - this.snMetadataRepo = snMetadataRepo; - this.expressionService = expressionService; - } - - public PlotData getPlotData(String dataType, String geneSymbol, String requestEnrollmentCategory) - throws JSONException, Exception { - JSONObject geneExpressionValues = expressionService.getGeneExpressionValues(dataType, geneSymbol); - FullDataTypeEnum dataTypeEnum = FullDataTypeEnum.fromAbbreviation(dataType); - List umapPoints = new ArrayList<>(); - EnrollmentCategoryEnum enrollmentCategory = EnrollmentCategoryEnum.fromRequestType(requestEnrollmentCategory); - - umapPoints = getUmapPoints(dataTypeEnum, umapPoints, enrollmentCategory); - - Map referenceClusters = new HashMap<>(); - FeatureData featureDataWithExpressionValues = new FeatureData(); - FeatureData featureDataWithNoExpressionValues = new FeatureData(); - - for (UmapPoint umapPoint : umapPoints) { - double umapX = umapPoint.getUmapX(); - double umapY = umapPoint.getUmapY(); - - if (referenceClusters.containsKey(umapPoint.getClusterAbbreviation())) { - ReferenceCluster referenceCluster = referenceClusters.get(umapPoint.getClusterAbbreviation()); - referenceCluster.addXValue(umapX); - referenceCluster.addYValue(umapY); - referenceCluster.setClusterName(umapPoint.getClusterName()); - referenceCluster.setClusterAbbreviation(umapPoint.getClusterAbbreviation()); - } else { - ReferenceCluster referenceCluster = new ReferenceCluster(umapPoint.getClusterAbbreviation(), - umapPoint.getClusterColor()); - referenceCluster.addXValue(umapX); - referenceCluster.addYValue(umapY); - referenceCluster.setClusterName(umapPoint.getClusterName()); - referenceCluster.setClusterAbbreviation(umapPoint.getClusterAbbreviation()); - referenceClusters.put(umapPoint.getClusterAbbreviation(), referenceCluster); - } - - String barcode = umapPoint.getBarcode(); - if (geneExpressionValues.has(barcode)) { - Double expressionValue = geneExpressionValues.getDouble(barcode); - featureDataWithExpressionValues.addXValue(umapX); - featureDataWithExpressionValues.addYValue(umapY); - featureDataWithExpressionValues.addExpression(expressionValue); - featureDataWithExpressionValues.addHoverDisplay(Double.toString(expressionValue) + "
" + umapPoint.getClusterName()); - - } else { - featureDataWithNoExpressionValues.addXValue(umapX); - featureDataWithNoExpressionValues.addYValue(umapY); - featureDataWithNoExpressionValues.addExpression(0d); - featureDataWithNoExpressionValues.addHoverDisplay(umapPoint.getClusterName()); - } - } - - if (dataTypeEnum.equals(FullDataTypeEnum.SINGLE_CELL) - && featureDataWithExpressionValues.getExpression().size() == 0 - && geneExpressionValues.length() <= 200) { - Iterator keys = geneExpressionValues.keys(); - while(keys.hasNext()) { - String barcode = keys.next(); - Double expressionValue = geneExpressionValues.getDouble(barcode); - UmapPoint umapPoint = scMetadataRepo.findByBarcode(barcode); - featureDataWithExpressionValues.addXValue(umapPoint.getUmapX()); - featureDataWithExpressionValues.addYValue(umapPoint.getUmapY()); - featureDataWithExpressionValues.addExpression(expressionValue); - featureDataWithExpressionValues.addHoverDisplay(Double.toString(expressionValue) + "
" + umapPoint.getClusterName()); - } - } - - List referenceClusterList = new ArrayList<>(referenceClusters.values()); - return new PlotData(referenceClusterList, - Arrays.asList(featureDataWithExpressionValues, featureDataWithNoExpressionValues)); - } - - private List getUmapPoints(FullDataTypeEnum dataTypeEnum, List umapPoints, - EnrollmentCategoryEnum enrollmentCategory) { - if (enrollmentCategory == EnrollmentCategoryEnum.ALL) { - if (dataTypeEnum.equals(FullDataTypeEnum.SINGLE_CELL)) { - int pointCount = scMetadataRepo.findCount(); - int limit = (int) Math.round(pointCount*.3); - umapPoints = scMetadataRepo.findLimited(limit); - } else if (dataTypeEnum.equals(FullDataTypeEnum.SINGLE_NUCLEUS)) { - int pointCount = snMetadataRepo.findCount(); - int limit = (int) Math.round(pointCount*.3); - umapPoints = snMetadataRepo.findLimited(limit); - } - } else if (enrollmentCategory != EnrollmentCategoryEnum.UNKNOWN) { - if (dataTypeEnum.equals(FullDataTypeEnum.SINGLE_CELL)) { - int pointCount = scMetadataRepo.findCount(); - int limit = (int) Math.round(pointCount*.3); - umapPoints = scMetadataRepo.findLimitedWithEnrollmentCategory(enrollmentCategory.getParticipantEnrollmentCategory(), limit); - } else if (dataTypeEnum.equals(FullDataTypeEnum.SINGLE_NUCLEUS)) { - int pointCount = snMetadataRepo.findCount(); - int limit = (int) Math.round(pointCount*.3); - umapPoints = snMetadataRepo.findLimitedWithEnrollmentCategory(enrollmentCategory.getParticipantEnrollmentCategory(), limit); - } - } - return umapPoints; - } - -} diff --git a/src/main/resources/graphql/knowledge_environment.graphqls b/src/main/resources/graphql/knowledge_environment.graphqls index 7c691a9c..73edc4df 100755 --- a/src/main/resources/graphql/knowledge_environment.graphqls +++ b/src/main/resources/graphql/knowledge_environment.graphqls @@ -1,24 +1,17 @@ type Query { autocomplete(searchTerm: String): [AutoCompleteResult] - cellTypeHierarchy: CellTypeHierarchy - cellTypeHierarchy2025: CellTypeHierarchy - geneExpressionSummary(dataType: String, geneSymbol: String, cellType: String, enrollmentCategory: String) : [GeneExpressionSummary] + cellTypeHierarchy2025: CellTypeHierarchy geneExpressionSummary2025(dataType: String, geneSymbol: String, cellType: String, enrollmentCategory: String) : [GeneExpressionSummary2025] - getClusterHieararchies(cellType: String!): [ClusterHierarchy] - getClusterHieararchies2025(cellType: String!): [ClusterHierarchy] - getUmapPlotData(dataType: String!, geneSymbol: String!, enrollmentCategory: String): PlotData + getClusterHieararchies2025(cellType: String!): [ClusterHierarchy] getUmapPlotData2025(dataType: String!, geneSymbol: String!, enrollmentCategory: String): PlotData2025 - dataTypesForConcept(geneSymbol: String, clusterName: String): [String] - dataTypesForConcept2025(geneSymbol: String, clusterName: String): [String] - getDataTypeSummaryInformation: [DataTypeSummaryInformation] + dataTypesForConcept2025(geneSymbol: String, clusterName: String): [String] getDataTypeSummaryInformation2025: [DataTypeSummaryInformation2025] getRTGeneExpressionByEnrollment(comparisonType: String, geneSymbol: String): RTGeneExpressionByEnrollment getRPGeneExpressionByEnrollment(geneSymbol: String!): [RPAccessionGroup] getRPGeneExpressionByEnrollmentAndProtein(geneSymbol: String!, protein: String!): RPExpressionByEnrollmentCategory getRTGeneExpressionByStructure(structure: String): [RTGeneExpression] getRPGeneExpressionByStructure(structure: String): [RPGeneExpression] - getSummaryData: [DataTypeSummaryInformation] - getDataTypeInformationByParticipant(redcapId: String!): ParticipantDataTypeSummary + getSummaryData: [DataTypeSummaryInformation2025] getDataTypeInformationByParticipant2025(redcapId: String!): ParticipantDataTypeSummary2025 getRepoDataTypeInformationByParticipant(redcapId: String!): ParticipantRepoDataTypeSummary participantSummaryDataset(redcapId: String!): ParticipantSummaryDataset @@ -28,6 +21,12 @@ type Query { getAtlasMessages: [AtlasMessages] getExperimentalStrategyCountsByParticipant(redcapId: String!): [ParticipantRepoDataTypeInformation] getParticipantClinicalDataset(redcapId: String!): ParticipantClinicalDataset + getHubmapTermMap: [HubmapOntologyCellType] +} + +type HubmapOntologyCellType { + hubmapOntologyId: String + cellType: String } type AtlasMessages { @@ -65,13 +64,8 @@ type ParticipantEnrollmentCategorySummary { dmrCount: Int } -type ParticipantDataTypeSummary { - spatialViewerDataTypes: [ParticipantDataTypeInformation] - explorerDataTypes: [ParticipantDataTypeInformation] -} - type ParticipantDataTypeSummary2025 { - spatialViewerDataTypes: [ParticipantDataTypeInformation] + spatialViewerDataTypes: [ParticipantDataTypeInformation2025] explorerDataTypes: [ParticipantDataTypeInformation2025] } @@ -81,14 +75,8 @@ type ParticipantDataTypeInformation2025 { isAggregatedData: Boolean } -type ParticipantDataTypeInformation { - dataType: String - count: Int - isAggregatedData: Boolean -} - type ParticipantRepoDataTypeSummary { - repositoryDataTypes: [ParticipantRepoDataTypeInformation] + repositoryDataTypes: [ParticipantDataTypeInformation2025] } type ParticipantRepoDataTypeInformation { @@ -109,20 +97,6 @@ type DataTypeSummaryInformation2025 { participantCount: Int } - -type DataTypeSummaryInformation { - omicsType: String - dataType: String - dataTypeShort: String - akiCount: Int - ckdCount: Int - hrtCount: Int - dmrCount: Int - totalCount: Int - participantCount: Int -} - - type AutoCompleteResult { value: String name: String @@ -149,22 +123,6 @@ type CellType { cellType: String } -type GeneExpressionSummary { - id: ID - enrollmentCategory: String - gene: String - pVal: Float - pValAdj: Float - foldChange: Float - pct1: Float - pct2: Float - avgExp: Float - cluster: String - clusterName: String - dataType: String - cellCount: Int -} - type GeneExpressionSummary2025 { id: ID enrollmentCategory: String @@ -192,6 +150,7 @@ type ClusterHierarchy { isSingleCellCluster: String isRegionalTranscriptomics: String isRegionalProteomics: String + isSpatialTranscriptomics: String cellTypeOrder: Float } @@ -215,26 +174,6 @@ type ReferenceCluster2025 { clusterAbbreviation: String } -type PlotData { - referenceData: [ReferenceCluster] - featureData: [FeatureData] -} - -type FeatureData { - xValues: [Float] - yValues: [Float] - expression: [Float] - hoverDisplay: [String] -} - -type ReferenceCluster { - xValues: [Float] - yValues: [Float] - color: String - clusterName: String - clusterAbbreviation: String -} - type RTGeneExpression { id: ID geneSymbol: String diff --git a/src/test/java/org/kpmp/QueryControllerTest.java b/src/test/java/org/kpmp/QueryControllerTest.java index a72acf34..f969822f 100755 --- a/src/test/java/org/kpmp/QueryControllerTest.java +++ b/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; @@ -22,8 +23,9 @@ 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; @@ -34,23 +36,13 @@ import org.kpmp.geneExpression.RTExpressionByEnrollmentCategory; import org.kpmp.geneExpression.RTExpressionDataAllSegments; import org.kpmp.geneExpression.RTExpressionDataService; -import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService; import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService2025; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionExpressionSummaryValue; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue; +import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionExpressionSummaryValue2025; import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue2025; -import org.kpmp.participant.ParticipantClinicalDataset; -import org.kpmp.participant.ParticipantDataTypeSummary; -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.FeatureData; import org.kpmp.umap.PlotData; import org.kpmp.umap.ReferenceCluster; -import org.kpmp.umap.UmapDataService; import org.kpmp.umap.UmapDataService2025; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -63,21 +55,17 @@ public class QueryControllerTest { @Mock private AutocompleteService autocompleteService; @Mock - private GeneExpressionSummaryService geneExpressionService; - @Mock private GeneExpressionSummaryService2025 geneExpressionService2025; @Mock private DataSummaryService dataSummaryService; private QueryController query; @Mock - private UmapDataService umapDataService; + private UmapDataService2025 umapDataService; @Mock private ClusterHierarchyService clusterHierarchyService; @Mock private RTExpressionDataService rtExpressionDataService; @Mock - private ParticipantService participantService; - @Mock private ParticipantEnrollmentCategorySummary participantEnrollmentCategorySummary; @Mock private AtlasMessageService atlasMessageService; @@ -89,13 +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, umapDataService, umapDataService2025, geneExpressionService, + query = new QueryController(autocompleteService, cellTypeService, umapDataService2025, geneExpressionService2025, dataSummaryService, clusterHierarchyService, rtExpressionDataService, rpExpressionDataService, - participantService, participantService2025, atlasMessageService); + participantService2025, atlasMessageService, hubmapCellTypeMappingService); } @AfterEach @@ -132,50 +122,12 @@ public void testAutocomplete() throws Exception { assertEquals(expectedResults, query.autocomplete("autocomplete")); } - @Test - public void testGetCellTypeHierarchy() throws Exception { - CellTypeHierarchy expectedResult = new CellTypeHierarchy(); - when(cellTypeService.getCellTypeHierarchy()).thenReturn(expectedResult); - - assertEquals(expectedResult, query.cellTypeHierarchy()); - } - - @SuppressWarnings({ "rawtypes", "unchecked" }) - @Test - public void geneExpression() throws Exception { - List expectedResultSN1 = Arrays.asList(new SNRNAGeneExpressionExpressionSummaryValue()); - List expectedResultSN2 = Arrays.asList(new SNRNAGeneExpressionExpressionSummaryValue()); - List expectedResultSN3 = Arrays.asList(new SNRNAGeneExpressionExpressionSummaryValue()); - List expectedResultSN4 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue()); - when(geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sn", "gene", "aki")).thenReturn(expectedResultSN1); - when(geneExpressionService.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sn", "cell type", "aki")) - .thenReturn(expectedResultSN2); - - when(geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sn", "gene", "aki")).thenReturn(expectedResultSN3); - when(geneExpressionService.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sn", "cell type", "aki")) - .thenReturn(expectedResultSN4); - - List expectedResultSC1 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue()); - List expectedResultSC2 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue()); - when(geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sc", "gene", "aki")).thenReturn(expectedResultSC1); - when(geneExpressionService.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sc", "cell type", "aki")) - .thenReturn(expectedResultSC2); - - assertEquals(expectedResultSN1, query.geneExpressionSummary("sn", "gene", "", "aki")); - assertEquals(expectedResultSC1, query.geneExpressionSummary("sc", "gene", "", "aki")); - - assertEquals(expectedResultSN2, query.geneExpressionSummary("sn", "", "cell type", "aki")); - assertEquals(expectedResultSC2, query.geneExpressionSummary("sc", "", "cell type", "aki")); - - assertEquals(expectedResultSN2, query.geneExpressionSummary("sn", "", "cell type", "aki")); - } - @Test public void geneExpression2025() throws Exception { List expectedResultSN1 = Arrays.asList(new SNRNAGeneExpressionExpressionSummaryValue2025()); List expectedResultSN2 = Arrays.asList(new SNRNAGeneExpressionExpressionSummaryValue2025()); List expectedResultSN3 = Arrays.asList(new SNRNAGeneExpressionExpressionSummaryValue2025()); - List expectedResultSN4 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue()); + List expectedResultSN4 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue2025()); when(geneExpressionService2025.getByDataTypeEnrollmentCategoryAndGene("sn", "gene", "aki")).thenReturn(expectedResultSN1); when(geneExpressionService2025.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sn", "cell type", "aki")) .thenReturn(expectedResultSN2); @@ -184,38 +136,19 @@ public void geneExpression2025() throws Exception { when(geneExpressionService2025.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sn", "cell type", "aki")) .thenReturn(expectedResultSN4); - List expectedResultSC1 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue()); - List expectedResultSC2 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue()); + List expectedResultSC1 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue2025()); + List expectedResultSC2 = Arrays.asList(new SCRNAGeneExpressionExpressionSummaryValue2025()); when(geneExpressionService2025.getByDataTypeEnrollmentCategoryAndGene("sc", "gene", "aki")).thenReturn(expectedResultSC1); when(geneExpressionService2025.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sc", "cell type", "aki")) .thenReturn(expectedResultSC2); - assertEquals(expectedResultSN1, query.geneExpressionSummary("sn", "gene", "", "aki")); - assertEquals(expectedResultSC1, query.geneExpressionSummary("sc", "gene", "", "aki")); + assertEquals(expectedResultSN1, query.geneExpressionSummary2025("sn", "gene", "", "aki")); + assertEquals(expectedResultSC1, query.geneExpressionSummary2025("sc", "gene", "", "aki")); - assertEquals(expectedResultSN2, query.geneExpressionSummary("sn", "", "cell type", "aki")); - assertEquals(expectedResultSC2, query.geneExpressionSummary("sc", "", "cell type", "aki")); + assertEquals(expectedResultSN2, query.geneExpressionSummary2025("sn", "", "cell type", "aki")); + assertEquals(expectedResultSC2, query.geneExpressionSummary2025("sc", "", "cell type", "aki")); - assertEquals(expectedResultSN2, query.geneExpressionSummary("sn", "", "cell type", "aki")); - } - - @Test - public void testGetUmapPlotData() throws Exception { - List featureData = new ArrayList<>(); - List referenceData = new ArrayList<>(); - PlotData expectedPlotData1 = new PlotData(referenceData, featureData); - PlotData expectedPlotData2 = new PlotData(referenceData, featureData); - when(umapDataService.getPlotData("sn", "gene", "all")).thenReturn(expectedPlotData1); - when(umapDataService.getPlotData("sn", "gene", "all")).thenReturn(expectedPlotData2); - - PlotData umapPlotData1 = query.getUmapPlotData("sn", "gene", "all"); - PlotData umapPlotData2 = query.getUmapPlotData("sn", "gene", "all"); - - assertEquals(expectedPlotData1, umapPlotData1); - verify(umapDataService).getPlotData("sn", "gene", "all"); - - assertEquals(expectedPlotData2, umapPlotData2); - verify(umapDataService).getPlotData("sn", "gene", "all"); + assertEquals(expectedResultSN2, query.geneExpressionSummary2025("sn", "", "cell type", "aki")); } @Test @@ -240,42 +173,42 @@ public void testGetUmapPlotData2025() throws Exception { @Test public void testGetClusterHierarchies() throws Exception { List expectedList = Arrays.asList(new ClusterHierarchy()); - when(clusterHierarchyService.findClustersByCellType("cell type")).thenReturn(expectedList); + when(clusterHierarchyService.findClustersByCellType2025("cell type")).thenReturn(expectedList); - assertEquals(expectedList, query.getClusterHieararchies("cell type")); - verify(clusterHierarchyService).findClustersByCellType("cell type"); + assertEquals(expectedList, query.getClusterHieararchies2025("cell type")); + verify(clusterHierarchyService).findClustersByCellType2025("cell type"); } @Test public void dataTypesForConceptWhenGeneSymbolAndNullClusterName() throws Exception { List expectedResult1 = Arrays.asList("1", "2"); List expectedResult2 = Arrays.asList("3", "4"); - when(geneExpressionService.findDataTypesByGene("gene")).thenReturn(expectedResult1); + when(geneExpressionService2025.findDataTypesByGene("gene")).thenReturn(expectedResult1); - List dataTypesForConcept1 = query.dataTypesForConcept("gene", null); - List dataTypesForConcept2 = query.dataTypesForConcept("gene", null); + List dataTypesForConcept1 = query.dataTypesForConcept2025("gene", null); + List dataTypesForConcept2 = query.dataTypesForConcept2025("gene", null); assertEquals(expectedResult1, dataTypesForConcept1); - verify(clusterHierarchyService, times(0)).findDataTypesByClusterName(any(String.class)); + verify(clusterHierarchyService, times(0)).findDataTypesByClusterName2025(any(String.class)); assertEquals(expectedResult2, dataTypesForConcept2); - verify(clusterHierarchyService, times(0)).findDataTypesByClusterName(any(String.class)); + verify(clusterHierarchyService, times(0)).findDataTypesByClusterName2025(any(String.class)); } @Test public void dataTypesForConceptWhenGeneSymbolAndBlankClusterName() throws Exception { List expectedResult1 = Arrays.asList("1", "2"); List expectedResult2 = Arrays.asList("3", "4"); - when(geneExpressionService.findDataTypesByGene("gene")).thenReturn(expectedResult1); - when(geneExpressionService.findDataTypesByGene("gene")).thenReturn(expectedResult2); + when(geneExpressionService2025.findDataTypesByGene("gene")).thenReturn(expectedResult1); + when(geneExpressionService2025.findDataTypesByGene("gene")).thenReturn(expectedResult2); - List dataTypesForConcept1 = query.dataTypesForConcept("gene", ""); - List dataTypesForConcept2 = query.dataTypesForConcept("gene", ""); + List dataTypesForConcept1 = query.dataTypesForConcept2025("gene", ""); + List dataTypesForConcept2 = query.dataTypesForConcept2025("gene", ""); assertEquals(expectedResult1, dataTypesForConcept1); - verify(clusterHierarchyService, times(0)).findDataTypesByClusterName(any(String.class)); + verify(clusterHierarchyService, times(0)).findDataTypesByClusterName2025(any(String.class)); assertEquals(expectedResult2, dataTypesForConcept2); - verify(clusterHierarchyService, times(0)).findDataTypesByClusterName(any(String.class)); + verify(clusterHierarchyService, times(0)).findDataTypesByClusterName2025(any(String.class)); } @@ -283,33 +216,33 @@ public void dataTypesForConceptWhenGeneSymbolAndBlankClusterName() throws Except public void dataTypesForConceptWhenClusterNameAndNullGene() throws Exception { List expectedResult1 = Arrays.asList("1", "2"); List expectedResult2 = Arrays.asList("3", "4"); - when(clusterHierarchyService.findDataTypesByClusterName("cluster")).thenReturn(expectedResult1); - when(clusterHierarchyService.findDataTypesByClusterName("cluster")).thenReturn(expectedResult2); + when(clusterHierarchyService.findDataTypesByClusterName2025("cluster")).thenReturn(expectedResult1); + when(clusterHierarchyService.findDataTypesByClusterName2025("cluster")).thenReturn(expectedResult2); - List dataTypesForConcept1 = query.dataTypesForConcept(null, "cluster"); - List dataTypesForConcept2 = query.dataTypesForConcept(null, "cluster"); + List dataTypesForConcept1 = query.dataTypesForConcept2025(null, "cluster"); + List dataTypesForConcept2 = query.dataTypesForConcept2025(null, "cluster"); assertEquals(expectedResult1, dataTypesForConcept1); - verify(geneExpressionService, times(0)).findDataTypesByGene(any(String.class)); + verify(geneExpressionService2025, times(0)).findDataTypesByGene(any(String.class)); assertEquals(expectedResult2, dataTypesForConcept2); - verify(geneExpressionService, times(0)).findDataTypesByGene(any(String.class)); + verify(geneExpressionService2025, times(0)).findDataTypesByGene(any(String.class)); } @Test public void dataTypesForConceptWhenClusterNameAndBlankGene() throws Exception { List expectedResult1 = Arrays.asList("1", "2"); List expectedResult2 = Arrays.asList("3", "4"); - when(clusterHierarchyService.findDataTypesByClusterName("cluster")).thenReturn(expectedResult1); - when(clusterHierarchyService.findDataTypesByClusterName("cluster")).thenReturn(expectedResult2); + when(clusterHierarchyService.findDataTypesByClusterName2025("cluster")).thenReturn(expectedResult1); + when(clusterHierarchyService.findDataTypesByClusterName2025("cluster")).thenReturn(expectedResult2); - List dataTypesForConcept1 = query.dataTypesForConcept("", "cluster"); - List dataTypesForConcept2 = query.dataTypesForConcept("", "cluster"); + List dataTypesForConcept1 = query.dataTypesForConcept2025("", "cluster"); + List dataTypesForConcept2 = query.dataTypesForConcept2025("", "cluster"); assertEquals(expectedResult1, dataTypesForConcept1); - verify(geneExpressionService, times(0)).findDataTypesByGene(any(String.class)); + verify(geneExpressionService2025, times(0)).findDataTypesByGene(any(String.class)); assertEquals(expectedResult2, dataTypesForConcept2); - verify(geneExpressionService, times(0)).findDataTypesByGene(any(String.class)); + verify(geneExpressionService2025, times(0)).findDataTypesByGene(any(String.class)); } @Test @@ -323,7 +256,7 @@ public void getGeneDatasetInformation() throws Exception { expectedResult1.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), FullDataTypeEnum.SINGLE_NUCLEUS.getFullName(), FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0))); - when(geneExpressionService.getDataTypeSummaryInformation()).thenReturn(expectedResult1); + when(geneExpressionService2025.getDataTypeSummaryInformation()).thenReturn(expectedResult1); expectedResult2.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), FullDataTypeEnum.SINGLE_CELL.getFullName(), FullDataTypeEnum.SINGLE_CELL.getAbbreviation(), @@ -331,10 +264,10 @@ public void getGeneDatasetInformation() throws Exception { expectedResult2.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), FullDataTypeEnum.SINGLE_NUCLEUS.getFullName(), FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0))); - when(geneExpressionService.getDataTypeSummaryInformation()).thenReturn(expectedResult2); + when(geneExpressionService2025.getDataTypeSummaryInformation()).thenReturn(expectedResult2); - List datasetSummary1 = query.getDataTypeSummaryInformation(); - List datasetSummary2 = query.getDataTypeSummaryInformation(); + List datasetSummary1 = query.getDataTypeSummaryInformation2025(); + List datasetSummary2 = query.getDataTypeSummaryInformation2025(); assertEquals(expectedResult1, datasetSummary1); assertEquals(expectedResult2, datasetSummary2); @@ -371,13 +304,13 @@ public void testGetRPGeneExpressionByEnrollmentAndProtein() throws Exception { @Test public void testGetDataTypeInformationByParticipant() throws Exception { - ParticipantDataTypeSummary expected1 = mock(ParticipantDataTypeSummary.class); - ParticipantDataTypeSummary expected2 = mock(ParticipantDataTypeSummary.class); - when(participantService.getExperimentCounts("123")).thenReturn(expected1); - when(participantService.getExperimentCounts("123")).thenReturn(expected2); + ParticipantDataTypeSummary2025 expected1 = mock(ParticipantDataTypeSummary2025.class); + ParticipantDataTypeSummary2025 expected2 = mock(ParticipantDataTypeSummary2025.class); + when(participantService2025.getExperimentCounts("123")).thenReturn(expected1); + when(participantService2025.getExperimentCounts("123")).thenReturn(expected2); - ParticipantDataTypeSummary result1 = query.getDataTypeInformationByParticipant("123"); - ParticipantDataTypeSummary result2 = query.getDataTypeInformationByParticipant("123"); + ParticipantDataTypeSummary2025 result1 = query.getDataTypeInformationByParticipant2025("123"); + ParticipantDataTypeSummary2025 result2 = query.getDataTypeInformationByParticipant2025("123"); assertEquals(expected1, result1); assertEquals(expected2, result2); @@ -387,7 +320,7 @@ public void testGetDataTypeInformationByParticipant() throws Exception { @Test public void testGetRepoDataTypeInformationByParticipant() throws Exception { ParticipantRepoDataTypeSummary expected = mock(ParticipantRepoDataTypeSummary.class); - when(participantService.getDataTypeCounts("123")).thenReturn(expected); + when(participantService2025.getDataTypeCounts("123")).thenReturn(expected); ParticipantRepoDataTypeSummary result = query.getRepoDataTypeInformationByParticipant("123"); @@ -398,19 +331,19 @@ public void testGetRepoDataTypeInformationByParticipant() throws Exception { @Test public void testGetParticipantClincialDataset() throws Exception { ParticipantClinicalDataset expected = new ParticipantClinicalDataset(); - when(participantService.getParticipantClinicalDataset("participant_id")).thenReturn(expected); + when(participantService2025.getParticipantClinicalDataset("participant_id")).thenReturn(expected); assertEquals(expected, query.getParticipantClinicalDataset("participant_id")); - verify(participantService).getParticipantClinicalDataset("participant_id"); + verify(participantService2025).getParticipantClinicalDataset("participant_id"); } @Test public void testParticipantSummaryDataset() throws Exception { ParticipantSummaryDataset expected = new ParticipantSummaryDataset(); - when(participantService.getParticipantSummaryDataset("participant_id")).thenReturn(expected); + when(participantService2025.getParticipantSummaryDataset("participant_id")).thenReturn(expected); assertEquals(expected, query.participantSummaryDataset("participant_id")); - verify(participantService).getParticipantSummaryDataset("participant_id"); + verify(participantService2025).getParticipantSummaryDataset("participant_id"); } @Test @@ -446,10 +379,27 @@ public void testGetAtlasMessage() throws Exception { @Test public void testGetExperimentalStrategyCountsByParticipant() { List expectedResults = new ArrayList<>(); - when(participantService.getExperimentalStrategyCountsByParticipant("redcapId")).thenReturn(expectedResults); + when(participantService2025.getExperimentalStrategyCountsByParticipant("redcapId")).thenReturn(expectedResults); List result = query.getExperimentalStrategyCountsByParticipant("redcapId"); 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 expectedList = Arrays.asList(cellType1, cellType2); + when(hubmapCellTypeMappingService.buildHubmapIdToCellTypeMap()).thenReturn(expectedList); + + List result = query.getHubmapTermMap(); + assertEquals(expectedList, result); + verify(hubmapCellTypeMappingService).buildHubmapIdToCellTypeMap(); + } } \ No newline at end of file diff --git a/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java b/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java index 26b2b47c..1208996e 100755 --- a/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java +++ b/src/test/java/org/kpmp/cellType/CellTypeServiceTest.java @@ -31,28 +31,6 @@ public void tearDown() throws Exception { cellTypeRepo = null; } - @Test - public void testGetCellTypeHierarchy() { - ArrayList cellTypes = new ArrayList(); - CellType cellType1 = new CellType(); - cellType1.setCellType("cell type 1"); - cellType1.setStructureSubregion("subregion 1"); - cellType1.setStructureRegion("region 1"); - cellTypes.add(cellType1); - when(cellTypeRepo.findAllByCellTypeIsNotNullOrderByCellTypeOrdering()).thenReturn(cellTypes); - - CellTypeHierarchy cellTypeHierarchy = service.getCellTypeHierarchy(); - - assertEquals(1, cellTypeHierarchy.getCellTypeRegions().size()); - CellTypeStructureRegion region = cellTypeHierarchy.getCellTypeRegions().get(0); - assertEquals("region 1", region.getRegionName()); - assertEquals(1, region.getCellTypeSubregions().size()); - CellTypeStructureSubregion subregion = region.getCellTypeSubregions().get(0); - assertEquals("subregion 1", subregion.getSubregionName()); - assertEquals(1, subregion.getCellTypes().size()); - assertEquals("cell type 1", subregion.getCellTypes().get(0).getCellType()); - } - @Test public void testGetCellTypeHierarchy2025() { ArrayList cellTypes = new ArrayList(); diff --git a/src/test/java/org/kpmp/cellType/HubmapCellTypeMappingServiceTest.java b/src/test/java/org/kpmp/cellType/HubmapCellTypeMappingServiceTest.java new file mode 100644 index 00000000..b96c56c6 --- /dev/null +++ b/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 cellTypes = Arrays.asList(cellType1, cellType2); + when(repo.findAll()).thenReturn(cellTypes); + + List 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 result = service.buildHubmapIdToCellTypeMap(); + assertTrue(result.isEmpty()); + } +} diff --git a/src/test/java/org/kpmp/cellType/HubmapOntologyCellTypeTest.java b/src/test/java/org/kpmp/cellType/HubmapOntologyCellTypeTest.java new file mode 100644 index 00000000..5605fd83 --- /dev/null +++ b/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()); + } +} diff --git a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java index 37d8c396..b71878c7 100755 --- a/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java +++ b/src/test/java/org/kpmp/cellTypeSummary/ClusterHierarchyServiceTest.java @@ -33,187 +33,6 @@ public void tearDown() throws Exception { service = null; } - @Test - public void testFindClustersByCellType() { - List hierarchies = Arrays.asList(new ClusterHierarchy()); - when(clusterHierarchyRepo.findByCellType("cell type")).thenReturn(hierarchies); - - assertEquals(hierarchies, service.findClustersByCellType("cell type")); - } - - @Test - public void testFindClustersByCellType_remvoesDups() { - ClusterHierarchy clusterHierarchy1 = new ClusterHierarchy(); - clusterHierarchy1.setCellType("celltype"); - clusterHierarchy1.setClusterName("cluster"); - ClusterHierarchy clusterHierarchy2 = new ClusterHierarchy(); - clusterHierarchy2.setCellType("cluster"); - clusterHierarchy2.setClusterName("cluster"); - List hierarchies = Arrays.asList(clusterHierarchy1, clusterHierarchy2); - - when(clusterHierarchyRepo.findByCellType("cell type")).thenReturn(hierarchies); - - assertEquals(Arrays.asList(clusterHierarchy2), service.findClustersByCellType("cell type")); - } - - @Test - public void testFindClustersByCellType_remvoesDupsUnlessNull() { - ClusterHierarchy clusterHierarchy1 = new ClusterHierarchy(); - clusterHierarchy1.setCellType("celltype"); - clusterHierarchy1.setClusterName(null); - clusterHierarchy1.setCellTypeOrder(3.2); - ClusterHierarchy clusterHierarchy2 = new ClusterHierarchy(); - clusterHierarchy2.setCellType("cluster"); - clusterHierarchy2.setClusterName(null); - clusterHierarchy2.setCellTypeOrder(2.0); - List hierarchies = Arrays.asList(clusterHierarchy1, clusterHierarchy2); - when(clusterHierarchyRepo.findByCellType("cell type")).thenReturn(hierarchies); - List expected = Arrays.asList(clusterHierarchy1, clusterHierarchy2); - - List result = service.findClustersByCellType("cell type"); - - assertEquals(expected.size(), result.size()); - assertEquals(true, result.containsAll(expected)); - } - - @Test - public void testFindClustersByCellType_sorts() { - ClusterHierarchy clusterHierarchy1 = new ClusterHierarchy(); - clusterHierarchy1.setCellType("celltype"); - clusterHierarchy1.setStructureSubregion("second region"); - clusterHierarchy1.setClusterName("cluster"); - clusterHierarchy1.setCellTypeOrder(5.0); - ClusterHierarchy clusterHierarchy2 = new ClusterHierarchy(); - clusterHierarchy2.setCellType("cluster"); - clusterHierarchy2.setClusterName("another cluster"); - clusterHierarchy2.setStructureSubregion("first region"); - clusterHierarchy2.setCellTypeOrder(1.0); - - List hierarchies = Arrays.asList(clusterHierarchy1, clusterHierarchy2); - - when(clusterHierarchyRepo.findByCellType("cell type")).thenReturn(hierarchies); - - assertEquals(Arrays.asList(clusterHierarchy2, clusterHierarchy1), service.findClustersByCellType("cell type")); - } - - @Test - public void testFindDataTypesByClusterNameWhenBothY() throws Exception { - ClusterHierarchy clusterHierarchy = new ClusterHierarchy(); - clusterHierarchy.setIsSingleCellCluster("Y"); - clusterHierarchy.setIsSingleNucCluster("Y"); - clusterHierarchy.setIsRegionalTranscriptomics("N"); - clusterHierarchy.setIsRegionalProteomics("N"); - when(clusterHierarchyRepo.findFirstByClusterOrRegion("cluster")).thenReturn(clusterHierarchy); - - List dataTypes = service.findDataTypesByClusterName("cluster"); - - assertEquals(2, dataTypes.size()); - assertEquals(Arrays.asList(FullDataTypeEnum.SINGLE_CELL.getAbbreviation(), - FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()), dataTypes); - verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster"); - } - - @Test - public void testFindDataTypesByClusterNameWhenSingleCellY() throws Exception { - ClusterHierarchy clusterHierarchy = new ClusterHierarchy(); - clusterHierarchy.setIsSingleCellCluster("Y"); - clusterHierarchy.setIsSingleNucCluster("N"); - clusterHierarchy.setIsRegionalTranscriptomics("N"); - clusterHierarchy.setIsRegionalProteomics("N"); - when(clusterHierarchyRepo.findFirstByClusterOrRegion("cluster")).thenReturn(clusterHierarchy); - - List dataTypes = service.findDataTypesByClusterName("cluster"); - - assertEquals(1, dataTypes.size()); - assertEquals(Arrays.asList(FullDataTypeEnum.SINGLE_CELL.getAbbreviation()), dataTypes); - verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster"); - } - - @Test - public void testFindDataTypesByClusterNameWhenSingleNucY() throws Exception { - ClusterHierarchy clusterHierarchy = new ClusterHierarchy(); - clusterHierarchy.setIsSingleCellCluster("N"); - clusterHierarchy.setIsSingleNucCluster("y"); - clusterHierarchy.setIsRegionalTranscriptomics("N"); - clusterHierarchy.setIsRegionalProteomics("N"); - when(clusterHierarchyRepo.findFirstByClusterOrRegion("cluster")).thenReturn(clusterHierarchy); - - List dataTypes = service.findDataTypesByClusterName("cluster"); - - assertEquals(1, dataTypes.size()); - assertEquals(Arrays.asList(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()), dataTypes); - verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster"); - } - - @Test - public void testFindDataTypesByClusterNameWhenNeitherY() throws Exception { - ClusterHierarchy clusterHierarchy = new ClusterHierarchy(); - clusterHierarchy.setIsSingleCellCluster("N"); - clusterHierarchy.setIsSingleNucCluster("N"); - clusterHierarchy.setIsRegionalTranscriptomics("N"); - clusterHierarchy.setIsRegionalProteomics("N"); - when(clusterHierarchyRepo.findFirstByClusterOrRegion("cluster")).thenReturn(clusterHierarchy); - - List dataTypes = service.findDataTypesByClusterName("cluster"); - - assertEquals(0, dataTypes.size()); - verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster"); - } - - @Test - public void testFindDataTypesByClusterNameWhenRTY() throws Exception { - ClusterHierarchy clusterHierarchy = new ClusterHierarchy(); - clusterHierarchy.setIsSingleCellCluster("N"); - clusterHierarchy.setIsSingleNucCluster("N"); - clusterHierarchy.setIsRegionalTranscriptomics("Y"); - clusterHierarchy.setIsRegionalProteomics("N"); - when(clusterHierarchyRepo.findFirstByClusterOrRegion("cluster")).thenReturn(clusterHierarchy); - - List dataTypes = service.findDataTypesByClusterName("cluster"); - - assertEquals(1, dataTypes.size()); - verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster"); - } - - - @Test - public void testFindDataTypesByClusterNameWhenRPY() throws Exception { - ClusterHierarchy clusterHierarchy = new ClusterHierarchy(); - clusterHierarchy.setIsSingleCellCluster("N"); - clusterHierarchy.setIsSingleNucCluster("N"); - clusterHierarchy.setIsRegionalTranscriptomics("N"); - clusterHierarchy.setIsRegionalProteomics("Y"); - when(clusterHierarchyRepo.findFirstByClusterOrRegion("cluster")).thenReturn(clusterHierarchy); - - List dataTypes = service.findDataTypesByClusterName("cluster"); - - assertEquals(1, dataTypes.size()); - assertEquals(Arrays.asList("rp"), dataTypes); - verify(clusterHierarchyRepo).findFirstByClusterOrRegion("cluster"); - } - - @Test - public void testFindClustersByCellTypeTubulesOrInterstitium() throws Exception { - List clusterHierarchies = new ArrayList<>(); - when(clusterHierarchyRepo.findByCellType("Tubules")).thenReturn(clusterHierarchies); - when(clusterHierarchyRepo.findByCellType("Interstitium")).thenReturn(clusterHierarchies); - List clusters = service.findClustersByCellType("Tubules"); - assertEquals("Tubulo-interstitium", clusters.get(0).getStructureRegion()); - List clusters2 = service.findClustersByCellType("Interstitium"); - assertEquals("Tubulo-interstitium", clusters2.get(0).getStructureRegion()); - } - - @Test - public void testFindDataTypesByClusterNameTi() throws Exception { - List dataTypes = service.findDataTypesByClusterName("Tubulo-interstitium"); - assertTrue(dataTypes.contains(FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation())); - assertTrue(dataTypes.contains(FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation())); - assertFalse(dataTypes.contains(FullDataTypeEnum.SINGLE_CELL.getAbbreviation())); - assertFalse(dataTypes.contains(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation())); - } - - //////// 2025 Set - @Test public void testFindClustersByCellType2025() { @@ -433,6 +252,12 @@ public void testFindClustersByCellTypeTubulesOrInterstitium2025() throws Excepti assertEquals("Tubulo-interstitium", clusters2.get(0).getStructureRegion()); } + @Test + public void testfindClustersByCellType2025RemovesDupes() throws Exception { + List clusterHierarchies = new ArrayList<>(); + + } + @Test public void testFindDataTypesByClusterNameTi2025() throws Exception { List dataTypes = service.findDataTypesByClusterName2025("Tubulo-interstitium"); diff --git a/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java b/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java deleted file mode 100755 index 56296fdb..00000000 --- a/src/test/java/org/kpmp/geneExpression/ExpressionDataServiceTest.java +++ /dev/null @@ -1,74 +0,0 @@ -package org.kpmp.geneExpression; - -import static org.junit.jupiter.api.Assertions.fail; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; - -import org.json.JSONException; -import org.json.JSONObject; -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.mockito.Mock; -import org.mockito.MockitoAnnotations; - -public class ExpressionDataServiceTest { - - @Mock - private SNExpressionDataRepository snRepo; - @Mock - private SCExpressionDataRepository scRepo; - @Mock - private SNExpressionDataRepository2025 snRepo2025; - private SNSCExpressionDataService service; - - @BeforeEach - public void setUp() throws Exception { - MockitoAnnotations.openMocks(this); - service = new SNSCExpressionDataService(snRepo, scRepo); - } - - @AfterEach - public void tearDown() throws Exception { - MockitoAnnotations.openMocks(this).close(); - service = null; - } - - @Test - public void testGetGeneExpressionValuesWhenSingleNuc() throws JSONException, Exception { - SNExpressionData expressionData1 = mock(SNExpressionData.class); - SNExpressionData2025 expressionData2025 = mock(SNExpressionData2025.class); - JSONObject expectedResult1 = new JSONObject(); - JSONObject expectedResult2 = new JSONObject(); - when(expressionData1.getExpressionDataAsJson()).thenReturn(expectedResult1); - when(expressionData2025.getExpressionDataAsJson()).thenReturn(expectedResult2); - when(snRepo.findByGeneSymbol("geneSymbol")).thenReturn(expressionData1); - when(snRepo2025.findByGeneSymbol("geneSymbol")).thenReturn(expressionData2025); - - assertEquals(expectedResult1, service.getGeneExpressionValues("sn", "geneSymbol")); - assertEquals(expectedResult2, service.getGeneExpressionValues("sn", "geneSymbol")); - } - - @Test - public void testGetGeneExpressionValuesWhenSingleCell() throws JSONException, Exception { - SCExpressionData expressionData = mock(SCExpressionData.class); - JSONObject expectedResult = new JSONObject(); - when(expressionData.getExpressionDataAsJson()).thenReturn(expectedResult); - when(scRepo.findByGeneSymbol("geneSymbol")).thenReturn(expressionData); - - assertEquals(expectedResult, service.getGeneExpressionValues("sc", "geneSymbol")); - } - - @Test - public void testGetGeneExpressionValuesWhenOtherDataType() throws JSONException { - - try { - service.getGeneExpressionValues("garbage", "geneSymbol"); - fail("Should have thrown exception"); - } catch (Exception expected) { - assertEquals("Invalid data type: garbage", expected.getMessage()); - } - } - -} diff --git a/src/test/java/org/kpmp/geneExpression/RTExpressionDataIdTest.java b/src/test/java/org/kpmp/geneExpression/RTExpressionDataIdTest.java new file mode 100644 index 00000000..876c325f --- /dev/null +++ b/src/test/java/org/kpmp/geneExpression/RTExpressionDataIdTest.java @@ -0,0 +1,46 @@ +package org.kpmp.geneExpression; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotEquals; +import org.junit.jupiter.api.Test; + +class RTExpressionDataIdTest { + + @Test + void testGettersAndSetters() { + RTExpressionDataId idData = new RTExpressionDataId(); + + idData.setId(101); + idData.setGeneSymbol("SOD1"); + idData.setPVal(0.05); + + assertEquals(101, idData.getId()); + assertEquals("SOD1", idData.getGeneSymbol()); + assertEquals(0.05, idData.getPVal()); + } + + @Test + void testConstructor() { + RTExpressionDataId idData = new RTExpressionDataId(202, "GAPDH", 0.001); + + assertEquals(202, idData.getId()); + assertEquals("GAPDH", idData.getGeneSymbol()); + assertEquals(0.001, idData.getPVal()); + } + + @Test + void testEqualsAndHashCode() { + RTExpressionDataId id1 = new RTExpressionDataId(1, "ALB", 0.01); + RTExpressionDataId id2 = new RTExpressionDataId(1, "ALB", 0.01); + RTExpressionDataId id3 = new RTExpressionDataId(2, "ALB", 0.01); + RTExpressionDataId id4 = new RTExpressionDataId(1, "INS", 0.01); + + assertEquals(id1, id2); + assertNotEquals(id1, id3); + assertNotEquals(id1, id4); + assertNotEquals(null, id1); + + assertEquals(id1.hashCode(), id2.hashCode()); + assertNotEquals(id1.hashCode(), id3.hashCode()); + } +} diff --git a/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java b/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java deleted file mode 100755 index c71f2a1f..00000000 --- a/src/test/java/org/kpmp/geneExpression/SCExpressionDataTest.java +++ /dev/null @@ -1,44 +0,0 @@ -package org.kpmp.geneExpression; - -import static org.junit.jupiter.api.Assertions.*; - -import org.json.JSONObject; -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -public class SCExpressionDataTest { - - private SCExpressionData data; - - @BeforeEach - public void setUp() throws Exception { - data = new SCExpressionData(); - } - - @AfterEach - public void tearDown() throws Exception { - data = null; - } - - @Test - public void testSetGeneSymbol() { - data.setGeneSymbol("gene symbol"); - assertEquals("gene symbol", data.getGeneSymbol()); - } - - @Test - public void testSetExpressionString() { - data.setExpressionString("expression string"); - assertEquals("expression string", data.getExpressionString()); - } - - @Test - public void testGetExpressionDataAsJson() throws Exception { - data.setExpressionString("{'key': 'value'}"); - JSONObject expressionJson = data.getExpressionDataAsJson(); - - assertEquals("value", expressionJson.get("key")); - } - -} diff --git a/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java b/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java deleted file mode 100755 index 80afe5e7..00000000 --- a/src/test/java/org/kpmp/geneExpression/SNExpressionDataTest.java +++ /dev/null @@ -1,44 +0,0 @@ -package org.kpmp.geneExpression; - -import static org.junit.jupiter.api.Assertions.*; - -import org.json.JSONObject; -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -public class SNExpressionDataTest { - - private SNExpressionData data; - - @BeforeEach - public void setUp() throws Exception { - data = new SNExpressionData(); - } - - @AfterEach - public void tearDown() throws Exception { - data = null; - } - - @Test - public void testSetGeneSymbol() { - data.setGeneSymbol("gene symbol"); - assertEquals("gene symbol", data.getGeneSymbol()); - } - - @Test - public void testSetExpressionString() { - data.setExpressionString("expression string"); - assertEquals("expression string", data.getExpressionString()); - } - - @Test - public void testGetExpressionDataAsJson() throws Exception { - data.setExpressionString("{'key': 'value'}"); - JSONObject expressionJson = data.getExpressionDataAsJson(); - - assertEquals("value", expressionJson.get("key")); - } - -} diff --git a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java deleted file mode 100755 index f29510da..00000000 --- a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java +++ /dev/null @@ -1,283 +0,0 @@ -package org.kpmp.geneExpressionSummary; - -import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.FullDataTypeEnum; -import org.kpmp.dataSummary.DataTypeSummary; -import org.kpmp.geneExpression.RPExpressionDataRepository; -import org.kpmp.geneExpression.RTExpressionDataAllSegmentsRepository; -import org.kpmp.geneExpressionSummary.regionalProteomics.RPParticipantRepository; -import org.kpmp.geneExpressionSummary.regionalTranscriptomics.RTParticipantRepository; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionExpressionSummaryValue; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionSummaryRepository; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionSummaryRepository2025; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAParticipantRepository; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue2025; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionSummaryRepository; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionSummaryRepository2025; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAParticipantRepository; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAParticipantRepository2025; -import org.mockito.Mock; -import org.mockito.MockitoAnnotations; - -public class GeneExpressionSummaryServiceTest { - - private GeneExpressionSummaryService geneExpressionService; - @Mock - private SNRNAGeneExpressionSummaryRepository snrnaGeneExpressionRepository; - @Mock - private SCRNAGeneExpressionSummaryRepository scrnaGeneExpressionRepository; - @Mock - private SCRNAParticipantRepository scrnaParticipantRepository; - @Mock - private SNRNAParticipantRepository snrnaParticipantRepository; - @Mock - private RTExpressionDataAllSegmentsRepository rtExpressionDataAllSegmentsRepository; - @Mock - private RTParticipantRepository rtParticipantRepository; - - @Mock - RPExpressionDataRepository rpExpressionDataRepository; - - @Mock - private RPParticipantRepository rpParticipantRepository; - - @Mock - private SNRNAParticipantRepository2025 snrnaParticipantRepository2025; - - @Mock - private SNRNAGeneExpressionSummaryRepository2025 snrnaGeneExpressionRepository2025; - - @Mock - private SCRNAGeneExpressionSummaryRepository2025 scrnaGeneExpressionRepository2025; - - @BeforeEach - public void setUp() throws Exception { - MockitoAnnotations.openMocks(this); - geneExpressionService = new GeneExpressionSummaryService( - scrnaGeneExpressionRepository, - snrnaGeneExpressionRepository,snrnaGeneExpressionRepository2025,scrnaParticipantRepository, scrnaGeneExpressionRepository2025, snrnaParticipantRepository, - rtParticipantRepository, rtExpressionDataAllSegmentsRepository, rpExpressionDataRepository, rpParticipantRepository); - } - - @AfterEach - public void tearDown() throws Exception { - MockitoAnnotations.openMocks(this).close(); - geneExpressionService = null; - } - - @SuppressWarnings("rawtypes") - @Test - public void testGetByDataTypeEnrollmentCategoryAndGene() throws Exception { - List snResults = Arrays - .asList(new SNRNAGeneExpressionExpressionSummaryValue()); - when(snrnaGeneExpressionRepository.findByEnrollmentAndGeneAllClusters("gene", "AKI")).thenReturn(snResults); - List snResults2025 = Arrays - .asList(new SNRNAGeneExpressionExpressionSummaryValue2025()); - when(snrnaGeneExpressionRepository2025.findByEnrollmentAndGeneAllClusters("gene", "AKI")).thenReturn(snResults2025); - List scResults = Arrays - .asList(new SCRNAGeneExpressionExpressionSummaryValue()); - when(scrnaGeneExpressionRepository.findByEnrollmentAndGeneAllClusters("gene", "AKI")).thenReturn(scResults); - - List results = geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("", "gene", "AKI"); - - assertEquals(2, results.size()); - List resultsSC = geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sc", - "gene", "aki"); - assertEquals(scResults, resultsSC); - assertEquals("sc", resultsSC.get(0).getDataType()); - List resultsSN = geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sn", - "gene", "aki"); - assertEquals(snResults, resultsSN); - assertEquals("sn", resultsSN.get(0).getDataType()); - - } - - @SuppressWarnings("rawtypes") - @Test - public void testGetExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory() throws Exception { - List snResults = Arrays - .asList(new SNRNAGeneExpressionExpressionSummaryValue()); - when(snrnaGeneExpressionRepository.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("cell type", "AKI")) - .thenReturn(snResults); - List snResults2025 = Arrays - .asList(new SNRNAGeneExpressionExpressionSummaryValue2025()); - when(snrnaGeneExpressionRepository2025.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("cell type", "AKI")) - .thenReturn(snResults2025); - List scResults = Arrays - .asList(new SCRNAGeneExpressionExpressionSummaryValue()); - when(scrnaGeneExpressionRepository.findExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("cell type", "AKI")) - .thenReturn(scResults); - - List results = geneExpressionService.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("", "cell type", "AKI"); - - assertEquals(2, results.size()); - List resultsSC = geneExpressionService - .getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sc", "cell type", "AKI"); - assertEquals(scResults, resultsSC); - assertEquals("sc", resultsSC.get(0).getDataType()); - List resultsSN = geneExpressionService - .getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sn", "cell type", "AKI"); - assertEquals(snResults, resultsSN); - assertEquals("sn", resultsSN.get(0).getDataType()); - List resultsSN2025 = geneExpressionService - .getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory("sn", "cell type", "AKI"); - assertEquals(snResults, resultsSN2025); - assertEquals("sn", resultsSN2025.get(0).getDataType()); - - - } - - @Test - public void testSCDuplicatesAreRemoved() throws Exception { - SCRNAGeneExpressionExpressionSummaryValue scv = new SCRNAGeneExpressionExpressionSummaryValue(); - SCRNAGeneExpressionExpressionSummaryValue scv2 = new SCRNAGeneExpressionExpressionSummaryValue(); - scv.setGene("gene"); - scv2.setGene("gene"); - scv.setCluster("cluster"); - scv2.setCluster("cluster"); - List summaryValues = new ArrayList<>(); - summaryValues.add(scv); - summaryValues.add(scv2); - when(scrnaGeneExpressionRepository.findByEnrollmentAndGeneAllClusters("gene", "all")).thenReturn(summaryValues); - - assertEquals(1, geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sc", "gene", "all").size()); - } - - @Test - public void testSNDuplicatesAreRemoved() throws Exception { - SNRNAGeneExpressionExpressionSummaryValue scv = new SNRNAGeneExpressionExpressionSummaryValue(); - SNRNAGeneExpressionExpressionSummaryValue scv2 = new SNRNAGeneExpressionExpressionSummaryValue(); - scv.setGene("gene"); - scv2.setGene("gene"); - scv.setCluster("cluster"); - scv2.setCluster("cluster"); - List summaryValues = new ArrayList<>(); - summaryValues.add(scv); - summaryValues.add(scv2); - when(snrnaGeneExpressionRepository.findByEnrollmentAndGeneAllClusters("gene", "all")).thenReturn(summaryValues); - - assertEquals(1, geneExpressionService.getByDataTypeEnrollmentCategoryAndGene("sn", "gene", "all").size()); - } - - @Test - public void testFindDataTypesByGeneWhenBothHaveData() throws Exception { - when(snrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(1l); - when(scrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(1l); - when(rtExpressionDataAllSegmentsRepository.getCountByGene("gene")).thenReturn(1l); - when(rpExpressionDataRepository.getCountByGene("gene")).thenReturn(1l); - - - List dataTypes = geneExpressionService.findDataTypesByGene("gene"); - - assertEquals(4, dataTypes.size()); - assertEquals(Arrays.asList(FullDataTypeEnum.SINGLE_CELL.getAbbreviation(), - FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(), FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation(), FullDataTypeEnum.REGIONAL_PROTEOMICS.getAbbreviation()), - dataTypes); - verify(snrnaGeneExpressionRepository).getCountByGene("gene"); - verify(scrnaGeneExpressionRepository).getCountByGene("gene"); - verify(rtExpressionDataAllSegmentsRepository).getCountByGene("gene"); - verify(rpExpressionDataRepository).getCountByGene("gene"); - } - - @Test - public void testFindDataTypesByGeneWhenSingleCellHasData() throws Exception { - when(snrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(0l); - when(scrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(1l); - when(rtExpressionDataAllSegmentsRepository.getCountByGene("gene")).thenReturn((long) 101); - - List dataTypes = geneExpressionService.findDataTypesByGene("gene"); - - assertEquals(2, dataTypes.size()); - assertEquals(Arrays.asList(FullDataTypeEnum.SINGLE_CELL.getAbbreviation(), - FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation()), dataTypes); - verify(snrnaGeneExpressionRepository).getCountByGene("gene"); - verify(scrnaGeneExpressionRepository).getCountByGene("gene"); - verify(rtExpressionDataAllSegmentsRepository).getCountByGene("gene"); - } - - @Test - public void testFindDataTypesByGeneWhenSingleNucHasData() throws Exception { - when(snrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(1l); - when(scrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(0l); - - List dataTypes = geneExpressionService.findDataTypesByGene("gene"); - - assertEquals(1, dataTypes.size()); - assertEquals(Arrays.asList(FullDataTypeEnum.SINGLE_NUCLEUS.getAbbreviation()), dataTypes); - verify(snrnaGeneExpressionRepository).getCountByGene("gene"); - verify(scrnaGeneExpressionRepository).getCountByGene("gene"); - } - - @Test - public void testFindDataTypesByGeneWhenNeitherHaveData() throws Exception { - when(snrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(0l); - when(scrnaGeneExpressionRepository.getCountByGene("gene")).thenReturn(0l); - - List dataTypes = geneExpressionService.findDataTypesByGene("gene"); - - assertEquals(0, dataTypes.size()); - assertEquals(Arrays.asList(), dataTypes); - verify(snrnaGeneExpressionRepository).getCountByGene("gene"); - verify(scrnaGeneExpressionRepository).getCountByGene("gene"); - } - - @Test - public void getDataTypeSummaryInformation() throws Exception { - - when(rtParticipantRepository.getCountByEnrollmentCategory("aki")).thenReturn((long) 0); - when(rtParticipantRepository.getCountByEnrollmentCategory("ckd")).thenReturn((long) 0); - when(rtParticipantRepository.getCountByEnrollmentCategory("hrt")).thenReturn((long) 0); - when(rtParticipantRepository.getParticipantCount()).thenReturn((long) 0); - when(scrnaGeneExpressionRepository.getCountByEnrollment("aki")).thenReturn(Long.valueOf(0)); - when(scrnaGeneExpressionRepository.getCountByEnrollment("ckd")).thenReturn(Long.valueOf(0)); - when(scrnaGeneExpressionRepository.getCountByEnrollment("hrt")).thenReturn(Long.valueOf(0)); - when(scrnaParticipantRepository.getParticipantCount()).thenReturn(Long.valueOf(0)); - when(snrnaGeneExpressionRepository.getCountByEnrollment("aki")).thenReturn(Long.valueOf(0)); - when(snrnaGeneExpressionRepository.getCountByEnrollment("ckd")).thenReturn(Long.valueOf(0)); - when(snrnaGeneExpressionRepository.getCountByEnrollment("hrt")).thenReturn(Long.valueOf(0)); - when(snrnaParticipantRepository.getParticipantCount()).thenReturn(Long.valueOf(0)); - when(rpParticipantRepository.getCountByEnrollmentCategory("aki")).thenReturn((long) 0); - when(rpParticipantRepository.getCountByEnrollmentCategory("ckd")).thenReturn((long) 0); - when(rpParticipantRepository.getCountByEnrollmentCategory("hrt")).thenReturn((long) 0); - when(rpParticipantRepository.getParticipantCount()).thenReturn((long) 0); - - List result = geneExpressionService.getDataTypeSummaryInformation(); - assertEquals(4, result.size()); - DataTypeSummary resultDataSC = result.get(0); - DataTypeSummary resultDataSN = result.get(1); - DataTypeSummary resultDataRt = result.get(2); - DataTypeSummary resultDataRp = result.get(3); - - assertEquals(Long.valueOf(0), resultDataSC.getAkiCount()); - assertEquals(Long.valueOf(0), resultDataSC.getCkdCount()); - assertEquals(Long.valueOf(0), resultDataSC.getHrtCount()); - assertEquals(Long.valueOf(0), resultDataSN.getAkiCount()); - assertEquals(Long.valueOf(0), resultDataSN.getCkdCount()); - assertEquals(Long.valueOf(0), resultDataRt.getHrtCount()); - assertEquals(Long.valueOf(0), resultDataRt.getAkiCount()); - assertEquals(Long.valueOf(0), resultDataRt.getCkdCount()); - assertEquals(Long.valueOf(0), resultDataRt.getHrtCount()); - assertEquals(Long.valueOf(0), resultDataRp.getHrtCount()); - assertEquals(Long.valueOf(0), resultDataRp.getAkiCount()); - assertEquals(Long.valueOf(0), resultDataRp.getCkdCount()); - assertEquals(Long.valueOf(0), resultDataRp.getHrtCount()); - - assertEquals("sc", resultDataSC.getDataTypeShort()); - assertEquals("sn", resultDataSN.getDataTypeShort()); - assertEquals("rt", resultDataRt.getDataTypeShort()); - assertEquals("rp", resultDataRp.getDataTypeShort()); - assertEquals(Long.valueOf(0), resultDataSN.getParticipantCount()); - - } -} diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java deleted file mode 100755 index 77086f09..00000000 --- a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionSummaryValueTest.java +++ /dev/null @@ -1,125 +0,0 @@ -package org.kpmp.geneExpressionSummary; - -import static org.junit.jupiter.api.Assertions.*; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionExpressionSummaryValue; - -public class SCRNAGeneExpressionSummaryValueTest { - - private SCRNAGeneExpressionExpressionSummaryValue scrnaGeneExpressionValue; - - @BeforeEach - public void setUp() throws Exception { - scrnaGeneExpressionValue = new SCRNAGeneExpressionExpressionSummaryValue(); - } - - @AfterEach - public void tearDown() throws Exception { - scrnaGeneExpressionValue = null; - } - - @Test - public void testGetDataType() throws Exception { - assertEquals("sc", scrnaGeneExpressionValue.getDataType()); - } - - @SuppressWarnings("null") - @Test - public void testSetAvgExpression() throws Exception { - scrnaGeneExpressionValue.setAvgExp(0.1); - assertEquals(0.1, scrnaGeneExpressionValue.getAvgExp(), 0.001); - - } - - @Test - public void testSetCluster() throws Exception { - scrnaGeneExpressionValue.setCluster("cluster"); - assertEquals("cluster", scrnaGeneExpressionValue.getCluster()); - } - - @SuppressWarnings("null") - @Test - public void testSetFoldChange() throws Exception { - scrnaGeneExpressionValue.setFoldChange(0.2); - assertEquals(0.2, scrnaGeneExpressionValue.getFoldChange(), 0.001); - } - - @Test - public void testSetGene() throws Exception { - scrnaGeneExpressionValue.setGene("gene"); - assertEquals("gene", scrnaGeneExpressionValue.getGene()); - - } - - @SuppressWarnings("null") - @Test - public void testSetId() throws Exception { - scrnaGeneExpressionValue.setId(1); - assertEquals(1, scrnaGeneExpressionValue.getId(), 0.001); - - } - - @SuppressWarnings("null") - @Test - public void testSetPct1() throws Exception { - scrnaGeneExpressionValue.setPct1(0.3); - assertEquals(0.3, scrnaGeneExpressionValue.getPct1(), 0.001); - - } - - @SuppressWarnings("null") - @Test - public void testSetPct2() throws Exception { - scrnaGeneExpressionValue.setPct2(0.4); - assertEquals(0.4, scrnaGeneExpressionValue.getPct2(), 0.001); - - } - - @SuppressWarnings("null") - @Test - public void testSetPVal() throws Exception { - scrnaGeneExpressionValue.setPVal(0.5); - assertEquals(0.5, scrnaGeneExpressionValue.getPVal(), 0.001); - - } - - @SuppressWarnings("null") - @Test - public void testSetPValAdj() throws Exception { - scrnaGeneExpressionValue.setPValAdj(0.6); - assertEquals(0.6, scrnaGeneExpressionValue.getPValAdj(), 0.001); - - } - - @Test - public void testSetEnrollmentCategory() throws Exception { - scrnaGeneExpressionValue.setEnrollmentCategory("tissue"); - assertEquals("tissue", scrnaGeneExpressionValue.getEnrollmentCategory()); - } - - @Test - public void testSetClusterName() throws Exception { - scrnaGeneExpressionValue.setClusterName("cluster name"); - assertEquals("cluster name", scrnaGeneExpressionValue.getClusterName()); - } - - @Test - public void testSetCellCount() throws Exception { - scrnaGeneExpressionValue.setCellCount(42); - assertEquals(Integer.valueOf(42), scrnaGeneExpressionValue.getCellCount()); - } - - @Test - public void testEquals() throws Exception { - scrnaGeneExpressionValue.setGene("gene"); - scrnaGeneExpressionValue.setCluster("cluster"); - SCRNAGeneExpressionExpressionSummaryValue value = new SCRNAGeneExpressionExpressionSummaryValue(); - value.setGene("gene"); - value.setCluster("cluster"); - assertEquals(value, scrnaGeneExpressionValue); - } - -} diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java deleted file mode 100755 index bee73189..00000000 --- a/src/test/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValueTest.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.kpmp.geneExpressionSummary; - -import static org.junit.jupiter.api.Assertions.*; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.geneExpressionSummary.singleCell.SCRNAParticipantValue; - -public class SCRNAParticipantValueTest { - - SCRNAParticipantValue scrnaParticipantValue; - - @BeforeEach - public void setUp() throws Exception { - scrnaParticipantValue = new SCRNAParticipantValue(); - } - - @AfterEach - public void tearDown() throws Exception { - scrnaParticipantValue = null; - } - - @Test - public void testSetEnrollmentCategory() throws Exception { - scrnaParticipantValue.setEnrollmentCategory("aki"); - assertEquals("aki", scrnaParticipantValue.getEnrollmentCategory()); - } - - public void setRedcapId() throws Exception { - scrnaParticipantValue.setRedcapId("27-10039"); - assertEquals("27-10039", scrnaParticipantValue.getRedcapId()); - } - -} diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java deleted file mode 100755 index 3c6fc626..00000000 --- a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionSummaryValueTest.java +++ /dev/null @@ -1,117 +0,0 @@ -package org.kpmp.geneExpressionSummary; - -import static org.junit.jupiter.api.Assertions.*; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue; - -public class SNRNAGeneExpressionSummaryValueTest { - - SNRNAGeneExpressionExpressionSummaryValue snrnaGeneExpressionValue; - - @BeforeEach - public void setUp() throws Exception { - snrnaGeneExpressionValue = new SNRNAGeneExpressionExpressionSummaryValue(); - } - - @AfterEach - public void tearDown() throws Exception { - snrnaGeneExpressionValue = null; - } - - @Test - public void testGetDataType() throws Exception { - assertEquals("sn", snrnaGeneExpressionValue.getDataType()); - } - - @Test - public void testSetAvgExpression() throws Exception { - snrnaGeneExpressionValue.setAvgExp(0.1); - assertEquals(0.1, snrnaGeneExpressionValue.getAvgExp(), 0.001); - - } - - @Test - public void testSetCluster() throws Exception { - snrnaGeneExpressionValue.setCluster("cluster"); - assertEquals("cluster", snrnaGeneExpressionValue.getCluster()); - } - - @Test - public void testSetFoldChange() throws Exception { - snrnaGeneExpressionValue.setFoldChange(0.2); - assertEquals(0.2, snrnaGeneExpressionValue.getFoldChange(), 0.001); - } - - @Test - public void testSetGene() throws Exception { - snrnaGeneExpressionValue.setGene("gene"); - assertEquals("gene", snrnaGeneExpressionValue.getGene()); - - } - - @Test - public void testSetId() throws Exception { - snrnaGeneExpressionValue.setId(1); - assertEquals(1, snrnaGeneExpressionValue.getId(), 0.001); - - } - - @Test - public void testSetPct1() throws Exception { - snrnaGeneExpressionValue.setPct1(0.3); - assertEquals(0.3, snrnaGeneExpressionValue.getPct1(), 0.001); - - } - - @Test - public void testSetPct2() throws Exception { - snrnaGeneExpressionValue.setPct2(0.4); - assertEquals(0.4, snrnaGeneExpressionValue.getPct2(), 0.001); - - } - - @Test - public void testSetPVal() throws Exception { - snrnaGeneExpressionValue.setPVal(0.5); - assertEquals(0.5, snrnaGeneExpressionValue.getPVal(), 0.001); - - } - - @Test - public void testSetPValAdj() throws Exception { - snrnaGeneExpressionValue.setPValAdj(0.6); - assertEquals(0.6, snrnaGeneExpressionValue.getPValAdj(), 0.001); - - } - - @Test - public void testSetEnrollmentCategory() throws Exception { - snrnaGeneExpressionValue.setEnrollmentCategory("tissue"); - assertEquals("tissue", snrnaGeneExpressionValue.getEnrollmentCategory()); - } - - @Test - public void testSetClusterName() throws Exception { - snrnaGeneExpressionValue.setClusterName("cluster name"); - assertEquals("cluster name", snrnaGeneExpressionValue.getClusterName()); - } - - @Test - public void testSetCellCount() throws Exception { - snrnaGeneExpressionValue.setCellCount(42); - assertEquals(Integer.valueOf(42), snrnaGeneExpressionValue.getCellCount()); - } - - @Test - public void testEquals() throws Exception { - snrnaGeneExpressionValue.setGene("gene"); - snrnaGeneExpressionValue.setCluster("cluster"); - SNRNAGeneExpressionExpressionSummaryValue value = new SNRNAGeneExpressionExpressionSummaryValue(); - value.setGene("gene"); - value.setCluster("cluster"); - assertEquals(value, snrnaGeneExpressionValue); - } -} diff --git a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java b/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java deleted file mode 100755 index e359330a..00000000 --- a/src/test/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValueTest.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.kpmp.geneExpressionSummary; - -import static org.junit.jupiter.api.Assertions.*; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAParticipantValue; - -public class SNRNAParticipantValueTest { - - SNRNAParticipantValue snrnaParticipantValue; - - @BeforeEach - public void setUp() throws Exception { - snrnaParticipantValue = new SNRNAParticipantValue(); - } - - @AfterEach - public void tearDown() throws Exception { - snrnaParticipantValue = null; - } - - @Test - public void testSetEnrollmentCategory() throws Exception { - snrnaParticipantValue.setEnrollmentCategory("aki"); - assertEquals("aki", snrnaParticipantValue.getEnrollmentCategory()); - } - - public void setRedcapId() throws Exception { - snrnaParticipantValue.setRedcapId("27-10039"); - assertEquals("27-10039", snrnaParticipantValue.getRedcapId()); - } - -} diff --git a/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java b/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java index 203d0075..a3d20bed 100755 --- a/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java +++ b/src/test/java/org/kpmp/participant/ParticipantDataTypeSummaryTest.java @@ -12,11 +12,11 @@ public class ParticipantDataTypeSummaryTest { - private ParticipantDataTypeSummary summary; + private ParticipantDataTypeSummary2025 summary; @BeforeEach public void setUp() throws Exception { - summary = new ParticipantDataTypeSummary(); + summary = new ParticipantDataTypeSummary2025(); } @AfterEach @@ -26,7 +26,7 @@ public void tearDown() throws Exception { @Test public void testSetSpatialViewerDataTypes() { - List experimentInfo = Arrays.asList(mock(ParticipantDataTypeInformation.class)); + List experimentInfo = Arrays.asList(mock(ParticipantDataTypeInformation2025.class)); summary.setSpatialViewerDataTypes(experimentInfo); @@ -35,7 +35,7 @@ public void testSetSpatialViewerDataTypes() { @Test public void testSetExplorerDataType() { - List experimentInfo = Arrays.asList(mock(ParticipantDataTypeInformation.class)); + List experimentInfo = Arrays.asList(mock(ParticipantDataTypeInformation2025.class)); summary.setExplorerDataTypes(experimentInfo); diff --git a/src/test/java/org/kpmp/participant/ParticipantServiceTest.java b/src/test/java/org/kpmp/participant/ParticipantServiceTest.java deleted file mode 100755 index 73ab5869..00000000 --- a/src/test/java/org/kpmp/participant/ParticipantServiceTest.java +++ /dev/null @@ -1,334 +0,0 @@ -package org.kpmp.participant; - -import static org.junit.jupiter.api.Assertions.*; -import static org.junit.jupiter.api.Assertions.fail; -import static org.mockito.Mockito.lenient; -import static org.mockito.Mockito.verify; -import static org.mockito.Mockito.when; - -import java.util.Arrays; -import java.util.List; -import org.kpmp.EnrollmentCategoryEnum; -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.dataSummary.DataSummaryRepository; -import org.kpmp.geneExpressionSummary.regionalProteomics.RPParticipantRepository; -import org.kpmp.geneExpressionSummary.regionalTranscriptomics.RTParticipantRepository; -import org.mockito.ArgumentCaptor; -import org.mockito.Mock; -import org.mockito.MockitoAnnotations; -import org.springframework.test.util.ReflectionTestUtils; - -public class ParticipantServiceTest { - - private ParticipantService participantService; - @Mock - private ParticipantSummaryDatasetRepository participantSummaryDatasetRepository; - @Mock - private DataSummaryRepository dataSummaryRepo; - @Mock - private SpatialViewerTypeRepository svTypeRepo; - @Mock - private SingleCellMetadataRepository scMetadataRepo; - @Mock - private SingleNucleusMetadataRepository snMetadataRepo; - @Mock - private SingleNucleusMetadataRepository2025 snMetadataRepo2025; - @Mock - private RTParticipantRepository rtParticipantRepo; - @Mock - private ParticipantRepoDataRepository fileByParticipantRepo; - @Mock - private RPParticipantRepository rpParticipantRepository; - @Mock - private ParticipantClinicalDatasetRepository participantClinicalDatasetRepo; - - @BeforeEach - public void setUp() throws Exception { - MockitoAnnotations.openMocks(this); - participantService = new ParticipantService(dataSummaryRepo, svTypeRepo, scMetadataRepo, snMetadataRepo, - snMetadataRepo2025, rtParticipantRepo, participantSummaryDatasetRepository, rpParticipantRepository,fileByParticipantRepo, participantClinicalDatasetRepo); - } - - @AfterEach - public void tearDown() throws Exception { - MockitoAnnotations.openMocks(this).close(); - participantService = null; - } - - @Test - public void testGetParticipantClincialDataset() throws Exception { - ParticipantSummaryDataset newPart = new ParticipantSummaryDataset(); - newPart.setRedcapId("1234"); - newPart.setParticipantId(99); - - ParticipantClinicalDataset expectedResult = new ParticipantClinicalDataset(); - expectedResult.setA1c("40%"); - expectedResult.setAlbuminuria("very bad"); - expectedResult.setBaselineEgfr("no good"); - expectedResult.setDiabetesDuration("40-49 Years"); - expectedResult.setDiabetesHistory("Yes"); - expectedResult.setKdigoStage("Stage 4"); - expectedResult.setOnRaasBlockade("Yes"); - expectedResult.setParticipantClinicalId(0); - expectedResult.setParticipantId(99); - expectedResult.setProteinuria("proteinuria"); - expectedResult.setRace("alien from outer space"); - expectedResult.setAgeBinned("age"); - expectedResult.setTissueSource("tissueSource"); - expectedResult.setProtocol("protocol"); - expectedResult.setSampleType("sample"); - expectedResult.setSex("sex"); - - - - when(participantSummaryDatasetRepository.findIdByRedcapId(newPart.getRedcapId())).thenReturn(newPart.getParticipantId()); - - when(participantService.getParticipantClinicalDataset(newPart.getRedcapId())).thenReturn(expectedResult); - - ParticipantClinicalDataset result = participantService.getParticipantClinicalDataset("1234"); - - assertEquals(0, result.getParticipantClinicalId()); - assertEquals(99, result.getParticipantId()); - assertEquals("40%", result.getA1c()); - assertEquals("very bad", result.getAlbuminuria()); - assertEquals("no good", result.getBaselineEgfr()); - assertEquals("40-49 Years", result.getDiabetesDuration()); - assertEquals("Yes", result.getDiabetesHistory()); - assertEquals("Stage 4", result.getKdigoStage()); - assertEquals("Yes", result.getOnRaasBlockade()); - assertEquals("proteinuria", result.getProteinuria()); - assertEquals("alien from outer space", result.getRace()); - assertEquals("age", result.getAgeBinned()); - assertEquals("tissueSource", result.getTissueSource()); - assertEquals("protocol", result.getProtocol()); - assertEquals("sex", result.getSex()); - assertEquals("sample", result.getSampleType()); - } - - @Test - public void testGetParticipantSummaryDataset() throws Exception { - - ParticipantSummaryDataset expectedResult = new ParticipantSummaryDataset(); - expectedResult.setParticipantId(1); - expectedResult.setOldParticipantId("2"); - expectedResult.setRedcapId("3"); - expectedResult.setSex("4"); - expectedResult.setAgeBinned("5"); - expectedResult.setTissueSource("6"); - expectedResult.setProtocol("7"); - expectedResult.setSampleType("8"); - expectedResult.setEnrollmentCategory("9"); - - when(participantSummaryDatasetRepository.findByRedcapId("1")).thenReturn(expectedResult); - - when(participantService.getParticipantSummaryDataset("1")).thenReturn(expectedResult); - - ParticipantSummaryDataset result = participantService.getParticipantSummaryDataset("1"); - - assertEquals(1, result.getParticipantId()); - assertEquals("2", result.getOldParticipantId()); - assertEquals("3", result.getRedcapId()); - assertEquals("4", result.getSex()); - assertEquals("5", result.getAgeBinned()); - assertEquals("6", result.getTissueSource()); - assertEquals("7", result.getProtocol()); - assertEquals("8", result.getSampleType()); - assertEquals("9", result.getEnrollmentCategory()); - } - - @Test - public void testGetExperimentCounts() { - SpatialViewerDataType dataType1 = new SpatialViewerDataType(); - dataType1.setDataType("Light Microscopy"); - dataType1.setTableName("sv_file_v"); - SpatialViewerDataType dataType2 = new SpatialViewerDataType(); - dataType2.setDataType("Spatial Lipidomics"); - dataType2.setTableName("sv_link_v"); - when(svTypeRepo.findAll()).thenReturn(Arrays.asList(dataType1, dataType2)); - when(dataSummaryRepo.getParticipantSvFileDataTypeCount("redcapId", "Light Microscopy")).thenReturn(5); - when(dataSummaryRepo.getParticipantSvLinkDataTypeCount("redcapId", "Spatial Lipidomics")).thenReturn(2); - when(scMetadataRepo.existsByRedcapId("redcapId")).thenReturn(true); - when(snMetadataRepo.existsByRedcapId("redcapId")).thenReturn(true); - when(rtParticipantRepo.existsByRedcapId("redcapId")).thenReturn(true); - when(rpParticipantRepository.existsByRedcapId("redcapId")).thenReturn(true); - - ParticipantDataTypeSummary result = participantService.getExperimentCounts("redcapId"); - - List spatialViewerDataTypes = result.getSpatialViewerDataTypes(); - assertEquals(2, spatialViewerDataTypes.size()); - List explorerDataTypes = result.getExplorerDataTypes(); - assertEquals(4, explorerDataTypes.size()); - for (ParticipantDataTypeInformation participantDataTypeInformation : spatialViewerDataTypes) { - if (participantDataTypeInformation.getDataType().equals("Light Microscopy")) { - assertEquals(Integer.valueOf(5), participantDataTypeInformation.getCount()); - assertEquals(false, participantDataTypeInformation.isAggregatedData()); - } else if (participantDataTypeInformation.getDataType().equals("Spatial Lipidomics")) { - assertEquals(Integer.valueOf(2), participantDataTypeInformation.getCount()); - assertEquals(false, participantDataTypeInformation.isAggregatedData()); - } - } - for (ParticipantDataTypeInformation participantDataTypeInformation : explorerDataTypes) { - assertEquals(Integer.valueOf(1), participantDataTypeInformation.getCount()); - assertEquals(true, participantDataTypeInformation.isAggregatedData()); - } - - ArgumentCaptor redcapIdCaptor = ArgumentCaptor.forClass(String.class); - ArgumentCaptor dataTypeCaptor = ArgumentCaptor.forClass(String.class); - verify(dataSummaryRepo).getParticipantSvFileDataTypeCount(redcapIdCaptor.capture(), dataTypeCaptor.capture()); - assertEquals("redcapId", redcapIdCaptor.getValue()); - assertEquals("Light Microscopy", dataTypeCaptor.getValue()); - verify(dataSummaryRepo).getParticipantSvLinkDataTypeCount(redcapIdCaptor.capture(), dataTypeCaptor.capture()); - assertEquals("redcapId", redcapIdCaptor.getValue()); - assertEquals("Spatial Lipidomics", dataTypeCaptor.getValue()); - - } - - @Test - public void testGetDataTypeCounts() throws Exception { - String dataType1 = "Transcriptomics", dataType2 = "Imaging"; - when(dataSummaryRepo.getRepoDataTypes()).thenReturn(Arrays.asList(dataType1, dataType2)); - when(dataSummaryRepo.getParticipantRepoFileDataTypeCount("redcapId", dataType1)).thenReturn(3); - when(dataSummaryRepo.getParticipantRepoFileDataTypeCount("redcapId", dataType2)).thenReturn(4); - - ParticipantRepoDataTypeSummary result = participantService.getDataTypeCounts("redcapId"); - - List repositoryDataTypes = result.getRepositoryDataTypes(); - assertEquals(2, repositoryDataTypes.size()); - for (ParticipantRepoDataTypeInformation participantDataTypeInformation : repositoryDataTypes) { - if(participantDataTypeInformation.getDataType().equals("Transcriptomics")) { - assertEquals(Integer.valueOf(3), participantDataTypeInformation.getCount()); - } - else if (participantDataTypeInformation.getDataType().equals("Imaging")) { - assertEquals(Integer.valueOf(4), participantDataTypeInformation.getCount()); - } - } - } - - @Test - public void testGetEnrollmentCounts() throws Exception { - when(participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.AKI.getParticipantEnrollmentCategory())).thenReturn(Long .valueOf(4)); - when(participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.CKD.getParticipantEnrollmentCategory())).thenReturn(Long .valueOf(5)); - when(participantSummaryDatasetRepository.getDataSummaryCount(EnrollmentCategoryEnum.HEALTHY_REFERENCE.getParticipantEnrollmentCategory())).thenReturn(Long .valueOf(6)); - - List result = participantService.getEnrollmentData(); - ParticipantEnrollmentCategorySummary resultDataAki = result.get(0); - ParticipantEnrollmentCategorySummary resultDataCkd = result.get(0); - ParticipantEnrollmentCategorySummary resultDataHrt = result.get(0); - - - assertEquals(Long.valueOf(4), resultDataAki.getAkiCount()); - assertEquals(Long.valueOf(5), resultDataCkd.getCkdCount()); - assertEquals(Long.valueOf(6), resultDataHrt.getHrtCount()); - } - - @Test - public void testGetTotalFilesCount() throws Exception { - when(dataSummaryRepo.getParticipantIDString("123")).thenReturn("abc"); - when(dataSummaryRepo.getParticipantTotalFileCount("abc")).thenReturn(5); - - ParticipantRepoDataTypeInformation result = participantService.getTotalFilesCount("123"); - - assertEquals(Integer.valueOf(5), result.getCount()); - assertEquals("redcap_id", result.getLinkInformation().getLinkType()); - assertEquals("123", result.getLinkInformation().getLinkValue()); - } - - @Test - public void testGetExperimentalStrategyCountsByParticipant() { - ParticipantRepoData experimentGroup1 = new ParticipantRepoData(); - experimentGroup1.setExperimentalStrategy("experiment1"); - experimentGroup1.setCount(1); - experimentGroup1.setDataCategory("something else"); - ParticipantRepoData experimentGroup2 = new ParticipantRepoData(); - experimentGroup2.setExperimentalStrategy(""); - experimentGroup2.setCount(2); - experimentGroup2.setDataType("Clinical Study Data"); - experimentGroup2.setDataCategory("another category"); - ParticipantRepoData experimentGroup3 = new ParticipantRepoData(); - experimentGroup3.setExperimentalStrategy("biomarker data"); - experimentGroup3.setDataCategory("Biomarker"); - experimentGroup3.setCount(3); - List experimentsByParticipant = Arrays.asList(experimentGroup1, experimentGroup2, experimentGroup3); - when(fileByParticipantRepo.findFileCountsByParticipant("participantId")).thenReturn(experimentsByParticipant); - ReflectionTestUtils.setField(participantService, "CLINICAL_STUDY_DATA", "Clinical Study Data"); - ReflectionTestUtils.setField(participantService, "BIOMARKERS", "Biomarkers"); - ReflectionTestUtils.setField(participantService, "BIOMARKER", "Biomarker"); - - List actualResults = participantService.getExperimentalStrategyCountsByParticipant("participantId"); - - assertEquals(3, actualResults.size()); - for (ParticipantRepoDataTypeInformation participantRepoDataTypeInformation : actualResults) { - if (participantRepoDataTypeInformation.getDataType().equals("experiment1")) { - assertEquals(Integer.valueOf(1), participantRepoDataTypeInformation.getCount()); - } else if (participantRepoDataTypeInformation.getDataType().equals("Clinical Study Data")) { - assertEquals(Integer.valueOf(2), participantRepoDataTypeInformation.getCount()); - } else if (participantRepoDataTypeInformation.getDataType().equals("Biomarkers")) { - assertEquals(Integer.valueOf(3), participantRepoDataTypeInformation.getCount()); - } else { - fail("unexpected data type: " + participantRepoDataTypeInformation.getDataType()); - } - } - } - - @Test - public void testGetExperimentalStrategyCountsByParticipant_combinesClinicalDataCounts() { - ParticipantRepoData experimentGroup1 = new ParticipantRepoData(); - experimentGroup1.setExperimentalStrategy(""); - experimentGroup1.setCount(1); - experimentGroup1.setDataType("Clinical Study Data"); - experimentGroup1.setDataCategory("something else"); - ParticipantRepoData experimentGroup2 = new ParticipantRepoData(); - experimentGroup2.setExperimentalStrategy(""); - experimentGroup2.setCount(2); - experimentGroup2.setDataType("Clinical Study Data"); - experimentGroup2.setDataCategory("another category"); - List experimentsByParticipant = Arrays.asList(experimentGroup1, experimentGroup2); - when(fileByParticipantRepo.findFileCountsByParticipant("participantId")).thenReturn(experimentsByParticipant); - ReflectionTestUtils.setField(participantService, "CLINICAL_STUDY_DATA", "Clinical Study Data"); - ReflectionTestUtils.setField(participantService, "BIOMARKERS", "Biomarkers"); - ReflectionTestUtils.setField(participantService, "BIOMARKER", "Biomarker"); - - List actualResults = participantService.getExperimentalStrategyCountsByParticipant("participantId"); - - assertEquals(1, actualResults.size()); - for (ParticipantRepoDataTypeInformation participantRepoDataTypeInformation : actualResults) { - if (participantRepoDataTypeInformation.getDataType().equals("Clinical Study Data")) { - assertEquals(Integer.valueOf(3), participantRepoDataTypeInformation.getCount()); - } else { - fail("unexpected data type: " + participantRepoDataTypeInformation.getDataType()); - } - } - } - - @Test - public void testGetExperimentalStrategyCountsByParticipant_combinesBiomarkerCounts() { - ParticipantRepoData experimentGroup1 = new ParticipantRepoData(); - experimentGroup1.setExperimentalStrategy("strat1"); - experimentGroup1.setCount(1); - experimentGroup1.setDataType("stuff"); - experimentGroup1.setDataCategory("Biomarker"); - ParticipantRepoData experimentGroup2 = new ParticipantRepoData(); - experimentGroup2.setExperimentalStrategy("strat2"); - experimentGroup2.setCount(2); - experimentGroup2.setDataType("more stuff"); - experimentGroup2.setDataCategory("Biomarker"); - List experimentsByParticipant = Arrays.asList(experimentGroup1, experimentGroup2); - when(fileByParticipantRepo.findFileCountsByParticipant("participantId")).thenReturn(experimentsByParticipant); - ReflectionTestUtils.setField(participantService, "CLINICAL_STUDY_DATA", "Clinical Study Data"); - ReflectionTestUtils.setField(participantService, "BIOMARKERS", "Biomarkers"); - ReflectionTestUtils.setField(participantService, "BIOMARKER", "Biomarker"); - - List actualResults = participantService.getExperimentalStrategyCountsByParticipant("participantId"); - - assertEquals(1, actualResults.size()); - for (ParticipantRepoDataTypeInformation participantRepoDataTypeInformation : actualResults) { - if (participantRepoDataTypeInformation.getDataType().equals("Biomarkers")) { - assertEquals(Integer.valueOf(3), participantRepoDataTypeInformation.getCount()); - } else { - fail("unexpected data type: " + participantRepoDataTypeInformation.getDataType()); - } - } - } -} \ No newline at end of file diff --git a/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java b/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java deleted file mode 100755 index 715d8f4f..00000000 --- a/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.kpmp.participant; - -import static org.junit.jupiter.api.Assertions.*; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -public class SingleCellMetadataTest { - - private SingleCellMetadata scMetadata; - - @BeforeEach - public void setUp() throws Exception { - scMetadata = new SingleCellMetadata(); - } - - @AfterEach - public void tearDown() throws Exception { - scMetadata = null; - } - - @Test - public void testSetBarcode() { - scMetadata.setBarcode("barcode"); - assertEquals("barcode", scMetadata.getBarcode()); - } - - @Test - public void testSetRedcapId() { - scMetadata.setRedcapId("redcapid"); - assertEquals("redcapid", scMetadata.getRedcapId()); - } - -} diff --git a/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java b/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java deleted file mode 100755 index 9b3420aa..00000000 --- a/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.kpmp.participant; - -import static org.junit.jupiter.api.Assertions.*; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -public class SingleNucleusMetadataTest { - - private SingleNucleusMetadata snMetadata; - - @BeforeEach - public void setUp() throws Exception { - snMetadata = new SingleNucleusMetadata(); - } - - @AfterEach - public void tearDown() throws Exception { - snMetadata = null; - } - - @Test - public void testSetBarcode() { - snMetadata.setBarcode("barcode"); - assertEquals("barcode", snMetadata.getBarcode()); - } - - @Test - public void testSetRedcapId() { - snMetadata.setRedcapId("redcapid"); - assertEquals("redcapid", snMetadata.getRedcapId()); - } - -} diff --git a/src/test/java/org/kpmp/umap/SCMetadataTest.java b/src/test/java/org/kpmp/umap/SCMetadataTest.java deleted file mode 100755 index 64610cfe..00000000 --- a/src/test/java/org/kpmp/umap/SCMetadataTest.java +++ /dev/null @@ -1,72 +0,0 @@ -package org.kpmp.umap; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -public class SCMetadataTest { - - private static double DOUBLE_PRECISION = 0.000001d; - private SCMetadata point; - - @BeforeEach - public void setUp() throws Exception { - point = new SCMetadata(); - } - - @AfterEach - public void tearDown() throws Exception { - point = null; - } - - @Test - public void testSetUmapX() { - point.setUmapX(2.4d); - assertEquals(2.4d, point.getUmapX(), DOUBLE_PRECISION); - } - - @Test - public void testSetUmapY() { - point.setUmapY(2.5d); - assertEquals(2.5d, point.getUmapY(), DOUBLE_PRECISION); - } - - @Test - public void testSetClusterName() { - point.setClusterName("cluster name"); - assertEquals("cluster name", point.getClusterName()); - } - - @Test - public void testSetClusterAbbreviation() { - point.setClusterAbbreviation("cluster abbr"); - assertEquals("cluster abbr", point.getClusterAbbreviation()); - } - - @Test - public void testSetClusterColor() { - point.setClusterColor("cluster color"); - assertEquals("cluster color", point.getClusterColor()); - } - - @Test - public void testSetExpressionValue() throws Exception { - point.setExpressionValue(4d); - assertEquals(4d, point.getExpressionValue(), DOUBLE_PRECISION); - } - - @Test - public void testSetBarcode() throws Exception { - point.setBarcode("barcode"); - assertEquals("barcode", point.getBarcode()); - } - - @Test - public void testSetEnrollmentCategory() throws Exception { - point.setEnrollmentCategory("enrollmentCategory"); - assertEquals("enrollmentCategory", point.getEnrollmentCategory()); - } - -} \ No newline at end of file diff --git a/src/test/java/org/kpmp/umap/SNMetadataTest.java b/src/test/java/org/kpmp/umap/SNMetadataTest.java deleted file mode 100755 index 884d81e6..00000000 --- a/src/test/java/org/kpmp/umap/SNMetadataTest.java +++ /dev/null @@ -1,72 +0,0 @@ -package org.kpmp.umap; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -public class SNMetadataTest { - - private static double DOUBLE_PRECISION = 0.000001d; - private SNMetadata point; - - @BeforeEach - public void setUp() throws Exception { - point = new SNMetadata(); - } - - @AfterEach - public void tearDown() throws Exception { - point = null; - } - - @Test - public void testSetUmapX() { - point.setUmapX(2.4d); - assertEquals(2.4d, point.getUmapX(), DOUBLE_PRECISION); - } - - @Test - public void testSetUmapY() { - point.setUmapY(2.5d); - assertEquals(2.5d, point.getUmapY(), DOUBLE_PRECISION); - } - - @Test - public void testSetClusterName() { - point.setClusterName("cluster name"); - assertEquals("cluster name", point.getClusterName()); - } - - @Test - public void testSetClusterAbbreviation() { - point.setClusterAbbreviation("cluster abbr"); - assertEquals("cluster abbr", point.getClusterAbbreviation()); - } - - @Test - public void testSetClusterColor() { - point.setClusterColor("cluster color"); - assertEquals("cluster color", point.getClusterColor()); - } - - @Test - public void testSetExpressionValue() throws Exception { - point.setExpressionValue(4d); - assertEquals(4d, point.getExpressionValue(), DOUBLE_PRECISION); - } - - @Test - public void testSetBarcode() throws Exception { - point.setBarcode("barcode"); - assertEquals("barcode", point.getBarcode()); - } - - @Test - public void testSetEnrollmentCategory() throws Exception { - point.setEnrollmentCategory("enrollmentCategory"); - assertEquals("enrollmentCategory", point.getEnrollmentCategory()); - } - -} diff --git a/src/test/java/org/kpmp/umap/UmapDataServiceTest.java b/src/test/java/org/kpmp/umap/UmapDataServiceTest.java deleted file mode 100755 index 6db738a8..00000000 --- a/src/test/java/org/kpmp/umap/UmapDataServiceTest.java +++ /dev/null @@ -1,169 +0,0 @@ -package org.kpmp.umap; - -import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.Mockito.when; - -import java.util.Arrays; -import java.util.List; - -import org.json.JSONObject; -import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.kpmp.geneExpression.SNSCExpressionDataService; -import org.kpmp.geneExpression.SNSCExpressionDataService2025; -import org.mockito.Mock; -import org.mockito.MockitoAnnotations; - -public class UmapDataServiceTest { - - private UmapDataService service; - @Mock - private SNSCExpressionDataService expressionDataService; - @Mock - private SNSCExpressionDataService2025 expressionDataService2025; - @Mock - private SCMetadataRepository scMetadataRepository; - @Mock - private SNMetadataRepository snMetadataRepository; - @Mock - private SNMetadataRepository2025 snMetadataRepository2025; - - private static double DOUBLE_PRECISION = 0.000001d; - - @BeforeEach - public void setUp() throws Exception { - MockitoAnnotations.openMocks(this); - service = new UmapDataService(scMetadataRepository, snMetadataRepository, expressionDataService); - } - - @AfterEach - public void tearDown() throws Exception { - MockitoAnnotations.openMocks(this).close(); - service = null; - } - - @Test - public void testGetPlotDataFeatureData() throws Exception { - SNMetadata snMetadata = new SNMetadata(); - snMetadata.setUmapX(3d); - snMetadata.setUmapY(4d); - snMetadata.setClusterName("clusterName"); - snMetadata.setClusterAbbreviation("clusterAbbrev"); - snMetadata.setBarcode("barcodeNotInExpression"); - SNMetadata snMetadata2 = new SNMetadata(); - snMetadata2.setUmapX(5d); - snMetadata2.setUmapY(6d); - snMetadata2.setClusterName("clusterName"); - snMetadata2.setClusterAbbreviation("clusterAbbrev"); - snMetadata2.setBarcode("barcode"); - List expectedPoints = Arrays.asList(snMetadata, snMetadata2); - when(snMetadataRepository.findCount()).thenReturn(7); - when(snMetadataRepository.findLimited(2)).thenReturn(expectedPoints); - when(expressionDataService.getGeneExpressionValues("sn", "gene")) - .thenReturn(new JSONObject("{ 'barcode': 0.4d , 'barcode2': 2.2d}")); - - PlotData plotData = service.getPlotData("sn", "gene", "all"); - - List featureData = plotData.getFeatureData(); - assertEquals(2, featureData.size()); - FeatureData featureDataWithExpressionValues = featureData.get(0); - assertEquals(1, featureDataWithExpressionValues.getXValues().size()); - assertEquals(1, featureDataWithExpressionValues.getXValues().size()); - assertEquals(5d, featureDataWithExpressionValues.getXValues().get(0), DOUBLE_PRECISION); - assertEquals(1, featureDataWithExpressionValues.getYValues().size()); - assertEquals(6d, featureDataWithExpressionValues.getYValues().get(0), DOUBLE_PRECISION); - assertEquals(1, featureDataWithExpressionValues.getExpression().size()); - assertEquals(0.4d, featureDataWithExpressionValues.getExpression().get(0), DOUBLE_PRECISION); - assertEquals("0.4
clusterName", featureDataWithExpressionValues.getHoverDisplay().get(0)); - - FeatureData featureDataWithZeroExpressionValue = featureData.get(1); - assertEquals(1, featureDataWithZeroExpressionValue.getXValues().size()); - assertEquals(3d, featureDataWithZeroExpressionValue.getXValues().get(0), DOUBLE_PRECISION); - assertEquals(1, featureDataWithZeroExpressionValue.getYValues().size()); - assertEquals(4d, featureDataWithZeroExpressionValue.getYValues().get(0), DOUBLE_PRECISION); - assertEquals(1, featureDataWithZeroExpressionValue.getExpression().size()); - assertEquals(0d, featureDataWithZeroExpressionValue.getExpression().get(0), DOUBLE_PRECISION); - assertEquals("clusterName", featureDataWithZeroExpressionValue.getHoverDisplay().get(0)); - - } - - @Test - public void testGetPlotDataReferenceDataOneCluster() throws Exception { - SNMetadata snMetadata = new SNMetadata(); - snMetadata.setUmapX(3d); - snMetadata.setUmapY(4d); - snMetadata.setClusterName("clusterName"); - snMetadata.setClusterAbbreviation("clusterAbbreviation"); - snMetadata.setClusterColor("color"); - snMetadata.setBarcode("barcodeNotInExpression"); - SNMetadata snMetadata2 = new SNMetadata(); - snMetadata2.setUmapX(5d); - snMetadata2.setUmapY(6d); - snMetadata2.setClusterName("clusterName"); - snMetadata2.setClusterAbbreviation("clusterAbbreviation"); - snMetadata2.setClusterColor("color"); - snMetadata2.setBarcode("barcode"); - List expectedPoints = Arrays.asList(snMetadata, snMetadata2); - when(snMetadataRepository.findCount()).thenReturn(7); - when(snMetadataRepository.findLimited(2)).thenReturn(expectedPoints); - when(expressionDataService.getGeneExpressionValues("sn", "gene")).thenReturn(new JSONObject()); - - PlotData plotData = service.getPlotData("sn", "gene", "all"); - - List clusters = plotData.getReferenceData(); - assertEquals(1, clusters.size()); - assertEquals("clusterAbbreviation", clusters.get(0).getClusterAbbreviation()); - assertEquals("color", clusters.get(0).getColor()); - List xValues = clusters.get(0).getXValues(); - assertEquals(2, xValues.size()); - assertEquals(3d, xValues.get(0), DOUBLE_PRECISION); - assertEquals(5d, xValues.get(1), DOUBLE_PRECISION); - List yValues = clusters.get(0).getYValues(); - assertEquals(2, yValues.size()); - assertEquals(4d, yValues.get(0), DOUBLE_PRECISION); - assertEquals(6d, yValues.get(1), DOUBLE_PRECISION); - - } - - @Test - public void testGetPlotDataReferenceDataMultipleClusters() throws Exception { - SNMetadata snMetadata = new SNMetadata(); - snMetadata.setUmapX(3d); - snMetadata.setUmapY(4d); - snMetadata.setClusterAbbreviation("clusterAbbrev1"); - snMetadata.setClusterColor("color1"); - snMetadata.setBarcode("barcodeNotInExpression"); - SNMetadata snMetadata2 = new SNMetadata(); - snMetadata2.setUmapX(5d); - snMetadata2.setUmapY(6d); - snMetadata2.setClusterAbbreviation("clusterAbbrev2"); - snMetadata2.setClusterColor("color2"); - snMetadata2.setBarcode("barcode"); - List expectedPoints = Arrays.asList(snMetadata, snMetadata2); - when(snMetadataRepository.findCount()).thenReturn(7); - when(snMetadataRepository.findLimited(2)).thenReturn(expectedPoints); - when(expressionDataService.getGeneExpressionValues("sn", "gene")).thenReturn(new JSONObject()); - - PlotData plotData = service.getPlotData("sn", "gene", "all"); - - List clusters = plotData.getReferenceData(); - assertEquals(2, clusters.size()); - assertEquals("clusterAbbrev2", clusters.get(0).getClusterAbbreviation()); - assertEquals("color2", clusters.get(0).getColor()); - assertEquals("clusterAbbrev1", clusters.get(1).getClusterAbbreviation()); - assertEquals("color1", clusters.get(1).getColor()); - List xValues = clusters.get(1).getXValues(); - assertEquals(1, xValues.size()); - assertEquals(3d, xValues.get(0), DOUBLE_PRECISION); - List yValues = clusters.get(1).getYValues(); - assertEquals(1, yValues.size()); - assertEquals(4d, yValues.get(0), DOUBLE_PRECISION); - xValues = clusters.get(0).getXValues(); - yValues = clusters.get(0).getYValues(); - assertEquals(5d, xValues.get(0), DOUBLE_PRECISION); - assertEquals(6d, yValues.get(0), DOUBLE_PRECISION); - - } - -}