Merge pull request #138 from KPMP/develop

Release v2.4

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

@@ -6,7 +6,7 @@ on:
 jobs:
   build-gradle-project:
     env:
-      IMAGE_TAG: 2.3.1
+      IMAGE_TAG: 2.4.0
     runs-on: ubuntu-latest
     steps:
       - name: Get branch names

build.gradle

@@ -21,7 +21,7 @@ apply plugin: 'io.spring.dependency-management'
 
 jar {
     baseName='pegasus-data'
-    version= '2.3.1'
+    version= '2.4.0'
 }
 
 repositories {

changelog.md

@@ -0,0 +1,14 @@
+# Changelog
+
+## Release 2.4 [unreleased]
+Brief summary of what's in this release:
+- added a total column to show total number of files for a grouping (needed back end because total includes groups not shown on atlas home page or explorer home page)
+
+### Breaking changes
+
+Breaking changes include any database updates needed, if we need to edit any files on system (like .env or certs, etc). Things that are outside of the code itself that need changed for the system to work.
+
+
+### Non-breaking changes
+
+Just a place to keep track of things that have changed in the code that we may want to pay special attention to when smoke testing, etc.

src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRow.java

@@ -7,6 +7,7 @@ public class AtlasRepoSummaryRow {
 	private Long ckdCount;
 	private Long hrtCount;
 	private Long dmrCount;
+	private Long totalCount;
 
 	public AtlasRepoSummaryRow(String omicsType, AtlasRepositoryLinkInformation linkInformation) {
 		this.omicsType = omicsType;
@@ -45,6 +46,14 @@ public void setDmrCount(Long dmrCount) {
 		this.dmrCount = dmrCount;
 	}
 
+	public Long getTotalCount() {
+		return this.totalCount;
+	}
+
+	public void setTotalCount(Long totalCount) {
+		this.totalCount = totalCount;
+	}
+
 	public String getOmicsType() {
 		return omicsType;
 	}

src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java

@@ -16,20 +16,39 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 			+ "join file f on f.file_id= fp.file_id " + "join sv_file_info sv on sv.file_id = f.file_id "
 			+ "where sv.config_type = :data_type " + "and p.tissue_type = :tissue_type", nativeQuery = true)
 	Long getDataSummaryCount(@Param("tissue_type") String tissue_type, @Param("data_type") String data_type);
+
+	@Cacheable("dataSummaryTotal")
+	@Query(value = "select count(distinct(redcap_id)) from participant p "
+			+ "join file_participant fp on p.participant_id = fp.participant_id "
+			+ "join file f on f.file_id= fp.file_id " + "join sv_file_info sv on sv.file_id = f.file_id "
+			+ "where sv.config_type = :data_type ", nativeQuery = true)
+	Long getDataSummaryTotal(@Param("data_type") String data_type);
 
 	@Cacheable("repoDataSummaryCount")
 	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where experimental_strategy = :exp_strat and tissue_type = :tissue_type", nativeQuery = true)
 	Long getRepoDataSummaryCount(@Param("tissue_type") String tissue_type, @Param("exp_strat") String exp_strat);
+
+	@Cacheable("repoDataSummaryTotal")
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where experimental_strategy = :exp_strat", nativeQuery = true)
+	Long getRepoDataSummaryTotal(@Param("exp_strat") String exp_strat);
 
 	@Cacheable("repoBiomarkerSummaryCount")
 	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where data_category = 'Biomarker' and tissue_type = :tissue_type", nativeQuery = true)
 	Long getRepoBiomarkerSummaryCount(@Param("tissue_type") String tissue_type);
+
+	@Cacheable("repoBiomarkerSummaryTotal")
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where data_category = 'Biomarker' ", nativeQuery = true)
+	Long getRepoBiomarkerSummaryTotal();
 
 	@Cacheable("dataSummaryLinkCount")
 	@Query(value = "select count(distinct(redcap_id)) " + "from sv_link_v " + "where data_type = :data_type "
 			+ "and tissue_type = :tissue_type", nativeQuery = true)
 	Long getDataSummaryLinkCount(@Param("tissue_type") String tissue_type, @Param("data_type") String data_type);
 
+	@Cacheable("dataSummaryLinkTotal")
+	@Query(value = "select count(distinct(redcap_id)) " + "from sv_link_v " + "where data_type = :data_type ", nativeQuery = true)
+	Long getDataSummaryLinkTotal(@Param("data_type") String data_type);
+
 	@Cacheable("dataParticipantSummaryCount")
 	@Query(value = "SELECT count(*) FROM sv_file_v WHERE data_type= :data_type", nativeQuery = true)
 	Long getParticipantSummaryCount(@Param("data_type") String data_type);

src/main/java/org/kpmp/dataSummary/DataSummaryService.java

@@ -110,6 +110,9 @@ private void setCounts(ExperimentalStrategyValue experimentalStrategyValue, Atla
 					TissueTypeEnum.DMR.getParticipantTissueType()
 				)
 			);
+			atlasRepoSummaryRow.setTotalCount(
+				dataSummaryRepository.getRepoBiomarkerSummaryTotal()
+			);
 		}
 		else {
 			atlasRepoSummaryRow.setAkiCount(
@@ -136,6 +139,11 @@ private void setCounts(ExperimentalStrategyValue experimentalStrategyValue, Atla
 					experimentalStrategyValue.getExperimentalStrategy()
 				)
 			);
+			atlasRepoSummaryRow.setTotalCount(
+				dataSummaryRepository.getRepoDataSummaryTotal(
+					experimentalStrategyValue.getExperimentalStrategy()
+				)
+			);
 		}
 	}
 
@@ -153,6 +161,7 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryTotal(FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()),
 				dataSummaryRepository
 						.getParticipantSummaryCount(FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName())));
 
@@ -167,6 +176,7 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryTotal(FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()),
 				dataSummaryRepository.getParticipantSummaryCount(
 						FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName())));
 
@@ -181,6 +191,8 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryTotal(
+						FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()),
 				dataSummaryRepository.getParticipantSummaryCount(
 						FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName())));
 
@@ -194,6 +206,7 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.CODEX_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.CODEX_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryTotal(FullDataTypeEnum.CODEX_FULL.getFullName()),
 				dataSummaryRepository.getParticipantSummaryCount(FullDataTypeEnum.CODEX_FULL.getFullName())));
 
 		summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(),
@@ -208,6 +221,7 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryLinkTotal(FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()),
 				dataSummaryRepository
 						.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName())));
 
@@ -223,6 +237,7 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryLinkTotal(FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()),
 				dataSummaryRepository
 						.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName())));
 
@@ -238,6 +253,7 @@ public List<DataTypeSummary> getSummaryData() {
 						FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()),
 				dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.DMR.getParticipantTissueType(),
 						FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryLinkTotal(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()),
 				dataSummaryRepository
 						.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName())));
 
@@ -253,6 +269,7 @@ public List<DataTypeSummary> getSummaryData() {
                         FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
                 dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
                         FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
+				dataSummaryRepository.getDataSummaryTotal(FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName()),
                 dataSummaryRepository
                         .getParticipantSummaryCount(FullDataTypeEnum.IMAGING_MASS_CYTOMETRY_FULL.getFullName())));
 		return summaryData;

src/main/java/org/kpmp/dataSummary/DataTypeSummary.java

@@ -12,6 +12,7 @@ public class DataTypeSummary implements Serializable {
 	private Long hrtCount;
 	private Long participantCount;
 	private Long dmrCount;
+	private Long totalCount;
 
 	public DataTypeSummary(String omicsType, String dataType, String dataTypeShort, Long akiCount, Long ckdCount,
 			Long hrtCount, Long dmrCount, Long participantCount) {
@@ -24,6 +25,19 @@ public DataTypeSummary(String omicsType, String dataType, String dataTypeShort,
 		this.dmrCount = dmrCount;
 		this.participantCount = participantCount;
 	}
+
+	public DataTypeSummary(String omicsType, String dataType, String dataTypeShort, Long akiCount, Long ckdCount,
+			Long hrtCount, Long dmrCount, Long totalCount, Long participantCount) {
+		this.omicsType = omicsType;
+		this.dataType = dataType;
+		this.dataTypeShort = dataTypeShort;
+		this.akiCount = akiCount;
+		this.ckdCount = ckdCount;
+		this.hrtCount = hrtCount;
+		this.dmrCount = dmrCount;
+		this.totalCount = totalCount;
+		this.participantCount = participantCount;
+	}
 
 	public String getOmicsType() {
 		return this.omicsType;
@@ -88,4 +102,12 @@ public Long getDmrCount() {
 	public void setDmrCount(Long dmrCount) {
 		this.dmrCount = dmrCount;
 	}
+
+	public Long getTotalCount() {
+		return this.totalCount;
+	}
+
+	public void setTotalCount(Long totalCount) {
+		this.totalCount = totalCount;
+	}
 }

src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java

@@ -135,6 +135,7 @@ public List<DataTypeSummary> getDataTypeSummaryInformation() {
 				scrnaGeneExpressionRepository
 						.getCountByTissue(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()),
 				scrnaGeneExpressionRepository.getCountByTissue(TissueTypeEnum.DMR.getParticipantTissueType()),
+				scrnaParticipantRepository.getParticipantCount(),
 				scrnaParticipantRepository.getParticipantCount()));
 		dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(),
 				FullDataTypeEnum.SINGLE_NUCLEUS_FULL.getFullName(), DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(),
@@ -143,6 +144,7 @@ public List<DataTypeSummary> getDataTypeSummaryInformation() {
 				snrnaGeneExpressionRepository
 						.getCountByTissue(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()),
 				snrnaGeneExpressionRepository.getCountByTissue(TissueTypeEnum.DMR.getParticipantTissueType()),
+				snrnaParticipantRepository.getParticipantCount(),
 				snrnaParticipantRepository.getParticipantCount()));
 		dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(),
 				FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS_FULL.getFullName(),
@@ -152,6 +154,7 @@ public List<DataTypeSummary> getDataTypeSummaryInformation() {
 				rtParticipantRepository
 						.getCountByTissueType(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()),
 				rtParticipantRepository.getCountByTissueType(TissueTypeEnum.DMR.getParticipantTissueType()),
+				rtParticipantRepository.getParticipantCount(),
 				rtParticipantRepository.getParticipantCount()));
 		dataTypeSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(),
 				FullDataTypeEnum.REGIONAL_PROTEOMICS_FULL.getFullName(),
@@ -161,6 +164,7 @@ public List<DataTypeSummary> getDataTypeSummaryInformation() {
 				rpParticipantRepository
 						.getCountByTissueType(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()),
 				rpParticipantRepository.getCountByTissueType(TissueTypeEnum.DMR.getParticipantTissueType()),
+				rpParticipantRepository.getParticipantCount(),
 				rpParticipantRepository.getParticipantCount()));
 		return dataTypeSummary;
 	}

src/main/resources/knowledge_environment.graphqls

@@ -40,6 +40,7 @@ type AtlasRepoSummaryRow {
   ckdCount: Long
   hrtCount: Long
   dmrCount: Long
+  totalCount: Long
   omicsType: String
   linkInformation: AtlasRepositoryLinkInformation
 }
@@ -85,6 +86,7 @@ type DataTypeSummaryInformation {
   ckdCount: Long
   hrtCount: Long
   dmrCount: Long
+  totalCount: Long
   participantCount: Long
 }