Merge pull request #150 from KPMP/KPMP-5618_add_enrollment_category

KPMP-5618: change tissue type to enrollment category

src/main/java/org/kpmp/TissueTypeEnum.java → src/main/java/org/kpmp/EnrollmentCategoryEnum.java

@@ -1,28 +1,28 @@
 package org.kpmp;
 
-public enum TissueTypeEnum {
+public enum EnrollmentCategoryEnum {
 
 	ALL("all", "all"), AKI("aki", "AKI"), CKD("ckd", "CKD"), HEALTHY_REFERENCE("hrt", "Healthy Reference"),
 	DMR("dmr", "DM-R"), UNKNOWN("", "");
 
 	private String requestType;
-	private String participantTissueType;
+	private String participantEnrollmentCategory;
 
-	private TissueTypeEnum(String requestType, String participantTissueType) {
+	private EnrollmentCategoryEnum(String requestType, String participantEnrollmentCategory) {
 		this.requestType = requestType;
-		this.participantTissueType = participantTissueType;
+		this.participantEnrollmentCategory = participantEnrollmentCategory;
 	}
 
-	public String getParticipantTissueType() {
-		return this.participantTissueType;
+	public String getParticipantEnrollmentCategory() {
+		return this.participantEnrollmentCategory;
 	}
 
     public String getRequestType() {
         return this.requestType;
     }
 
 
-    public static TissueTypeEnum fromRequestType(String requestType) {
+    public static EnrollmentCategoryEnum fromRequestType(String requestType) {
 		if (ALL.requestType.equalsIgnoreCase(requestType)) {
 			return ALL;
 		} else if (AKI.requestType.equalsIgnoreCase(requestType)) {

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

@@ -23,7 +23,7 @@
 import org.kpmp.participant.ParticipantRepoDataTypeSummary;
 import org.kpmp.participant.ParticipantService;
 import org.kpmp.participant.ParticipantSummaryDataset;
-import org.kpmp.participant.ParticipantTissueTypeSummary;
+import org.kpmp.participant.ParticipantEnrollmentCategorySummary;
 import org.kpmp.umap.PlotData;
 import org.kpmp.umap.UmapDataService;
 import org.slf4j.Logger;
@@ -82,13 +82,13 @@ public CellTypeHierarchy cellTypeHierarchy() throws IOException {
 
     @QueryMapping
 	public List<? extends GeneExpressionSummary> geneExpressionSummary(@Argument String dataType, @Argument String geneSymbol,
-        @Argument String cellType, @Argument String tissueType) throws IOException {
+        @Argument String cellType, @Argument String enrollmentCategory) throws IOException {
 		List<? extends GeneExpressionSummary> results = new ArrayList<>();
 		if (cellType.isEmpty()) {
-			results = geneExpressionSummaryService.getByDataTypeTissueTypeAndGene(dataType, geneSymbol, tissueType);
+			results = geneExpressionSummaryService.getByDataTypeEnrollmentCategoryAndGene(dataType, geneSymbol, enrollmentCategory);
 		} else if (geneSymbol.isEmpty()) {
-			results = geneExpressionSummaryService.getExpressionSummaryPerGeneByCellTypeAndTissueType(dataType,
-					cellType, tissueType);
+			results = geneExpressionSummaryService.getExpressionSummaryPerGeneByCellTypeAndEnrollmentCategory(dataType,
+					cellType, enrollmentCategory);
 		}
 		return results;
 	}
@@ -99,9 +99,9 @@ public List<ClusterHierarchy> getClusterHieararchies(@Argument String cellType)
 	}
 
     @QueryMapping
-	public PlotData getUmapPlotData(@Argument String dataType, @Argument String geneSymbol, @Argument String tissueType) throws Exception {
+	public PlotData getUmapPlotData(@Argument String dataType, @Argument String geneSymbol, @Argument String enrollmentCategory) throws Exception {
 		try {
-			return umapService.getPlotData(dataType, geneSymbol, tissueType);
+			return umapService.getPlotData(dataType, geneSymbol, enrollmentCategory);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
@@ -140,18 +140,18 @@ public List<String> dataTypesForConcept(@Argument String geneSymbol, @Argument S
 	}
 
     @QueryMapping
-	public RTExpressionByTissueType getRTGeneExpressionByTissue(@Argument String comparisonType, @Argument String geneSymbol)
+	public RTExpressionByEnrollmentCategory getRTGeneExpressionByTissue(@Argument String comparisonType, @Argument String geneSymbol)
 			throws Exception {
 		try {
-			return rtExpressionDataService.getByComparisonTypeAndGeneSymbolPerTissue(comparisonType, geneSymbol);
+			return rtExpressionDataService.getByComparisonTypeAndGeneSymbolPerEnrollment(comparisonType, geneSymbol);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
 		}
 	}
 
     @QueryMapping
-	public RPExpressionByTissueType getRPGeneExpressionByTissueAndProtein(@Argument String geneSymbol, @Argument String protein) throws Exception {
+	public RPExpressionByEnrollmentCategory getRPGeneExpressionByTissueAndProtein(@Argument String geneSymbol, @Argument String protein) throws Exception {
 		try {
 			return rpExpressionDataService.getByGeneSymbolAndProteinPerTissue(geneSymbol, protein);
 		} catch (Exception e) {
@@ -225,9 +225,9 @@ public ParticipantRepoDataTypeInformation getTotalParticipantFilesCount(@Argumen
 	}
 
     @QueryMapping
-	public List<ParticipantTissueTypeSummary> getTissueTypeSummaryData() throws Exception {
+	public List<ParticipantEnrollmentCategorySummary> getEnrollmentCategorySummaryData() throws Exception {
 		try {
-			return participantService.getTissueData();
+			return participantService.getEnrollmentData();
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;

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

@@ -14,9 +14,9 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 	@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 " + "and p.tissue_type = :tissue_type " 
+			+ "where sv.config_type = :data_type " + "and p.enrollment_category = :enrollment_category " 
 	       		+ "and sv.release_sunset_version is null", nativeQuery = true)
-	Long getDataSummaryCount(@Param("tissue_type") String tissue_type, @Param("data_type") String data_type);
+	Long getDataSummaryCount(@Param("enrollment_category") String enrollment_category, @Param("data_type") String data_type);
 
 	@Cacheable("dataSummaryTotal")
 	@Query(value = "select count(distinct(redcap_id)) from participant p "
@@ -26,25 +26,25 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 	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);
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where experimental_strategy = :exp_strat and enrollment_category = :enrollment_category", nativeQuery = true)
+	Long getRepoDataSummaryCount(@Param("enrollment_category") String enrollment_category, @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);
+	@Query(value = "select count(distinct(dl_file_id)) from repo_file_v where data_category = 'Biomarker' and enrollment_category = :enrollment_category", nativeQuery = true)
+	Long getRepoBiomarkerSummaryCount(@Param("enrollment_category") String enrollment_category);
 
 	@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);
+			+ "and enrollment_category = :enrollment_category", nativeQuery = true)
+	Long getDataSummaryLinkCount(@Param("enrollment_category") String enrollment_category, @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)