Merge pull request #125 from KPMP/KPMP-4861_update_getatlassummaryrows

KPMP-4861: Update endpoint to return counts for tissue type
KPMP · Feb 22, 2024 · 0d22891 · 0d22891
2 parents c54cd4a + 168a0b6
commit 0d22891
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Showing 7 changed files with 167 additions and 108 deletions.
diff --git a/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRow.java b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRow.java
@@ -1,46 +1,56 @@
 package org.kpmp.dataSummary;
 
 public class AtlasRepoSummaryRow {
-	private int openCount;
-	private int controlledCount;
 	private String omicsType;
 	private AtlasRepositoryLinkInformation linkInformation;
+	private Long akiCount;
+	private Long ckdCount;
+	private Long hrtCount;
+	private Long dmrCount;
 
 	public AtlasRepoSummaryRow(String omicsType, AtlasRepositoryLinkInformation linkInformation) {
 		this.omicsType = omicsType;
 		this.linkInformation = linkInformation;
 	}
 
-	public int getOpenCount() {
-		return openCount;
+	public Long getAkiCount() {
+		return this.akiCount;
 	}
 
-	public void setOpenCount(int openCount) {
-		this.openCount = openCount;
+	public void setAkiCount(Long akiCount) {
+		this.akiCount = akiCount;
 	}
 
-	public int getControlledCount() {
-		return controlledCount;
+	public Long getCkdCount() {
+		return this.ckdCount;
 	}
 
-	public void setControlledCount(int controlledCount) {
-		this.controlledCount = controlledCount;
+	public void setCkdCount(Long ckdCount) {
+		this.ckdCount = ckdCount;
 	}
 
-	public String getOmicsType() {
-		return omicsType;
+	public Long getHrtCount() {
+		return this.hrtCount;
 	}
 
-	public void setOmicsType(String omicsType) {
-		this.omicsType = omicsType;
+	public void setHrtCount(Long hrtCount) {
+		this.hrtCount = hrtCount;
+	}
+
+	public Long getDmrCount() {
+		return this.dmrCount;
 	}
 
-	public void addToControlledCount(int count) {
-		this.controlledCount = this.controlledCount + count;
+	public void setDmrCount(Long dmrCount) {
+		this.dmrCount = dmrCount;
 	}
 
-	public void addToOpenCount(int count) {
-		this.openCount = this.openCount + count;
+	public String getOmicsType() {
+		return omicsType;
+	}
+
+	public void setOmicsType(String omicsType) {
+		this.omicsType = omicsType;
 	}
 
 	public AtlasRepositoryLinkInformation getLinkInformation() {

diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java b/src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java
@@ -16,6 +16,10 @@ 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("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("dataSummaryLinkCount")
 	@Query(value = "select count(distinct(redcap_id)) " + "from sv_link_v " + "where data_type = :data_type "

diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java
@@ -89,14 +89,30 @@ private AtlasRepositoryLinkInformation getLinkInformation(ExperimentalStrategyVa
 
 	private void setCounts(ExperimentalStrategyValue experimentalStrategyValue, AtlasRepoSummaryRow atlasRepoSummaryRow)
 			throws Exception {
-		if (experimentalStrategyValue.getAccess().equalsIgnoreCase(OPEN_ACCESS)) {
-			atlasRepoSummaryRow.addToOpenCount(experimentalStrategyValue.getCount());
-		} else if (experimentalStrategyValue.getAccess().equalsIgnoreCase(CONTROLLED_ACCESS)) {
-			atlasRepoSummaryRow.addToControlledCount(experimentalStrategyValue.getCount());
-		} else {
-			throw new Exception(
-					"Unexpected access value while getting summary counts: " + experimentalStrategyValue.getAccess());
-		}
+		atlasRepoSummaryRow.setAkiCount(
+			dataSummaryRepository.getRepoDataSummaryCount(
+				TissueTypeEnum.AKI.getParticipantTissueType(), 
+				experimentalStrategyValue.getExperimentalStrategy()
+			)
+		);
+		atlasRepoSummaryRow.setCkdCount(
+			dataSummaryRepository.getRepoDataSummaryCount(
+				TissueTypeEnum.CKD.getParticipantTissueType(), 
+				experimentalStrategyValue.getExperimentalStrategy()
+			)
+		);
+		atlasRepoSummaryRow.setHrtCount(
+			dataSummaryRepository.getRepoDataSummaryCount(
+				TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), 
+				experimentalStrategyValue.getExperimentalStrategy()
+			)
+		);
+		atlasRepoSummaryRow.setDmrCount(
+			dataSummaryRepository.getRepoDataSummaryCount(
+				TissueTypeEnum.DMR.getParticipantTissueType(), 
+				experimentalStrategyValue.getExperimentalStrategy()
+			)
+		);
 	}
 
 	public List<DataTypeSummary> getSummaryData() {

diff --git a/src/main/resources/knowledge_environment.graphqls b/src/main/resources/knowledge_environment.graphqls
@@ -36,13 +36,15 @@ type AtlasRepoSummaryResult {
 }
 
 type AtlasRepoSummaryRow {
-  openCount: Int
-  controlledCount: Int
+  akiCount: Long
+  ckdCount: Long
+  hrtCount: Long
+  dmrCount: Long
   omicsType: String
-  linkInformation: AtlasRepoSummaryLinkInformation
+  linkInformation: AtlasRepositoryLinkInformationInformation
 }
 
-type AtlasRepoSummaryLinkInformation {
+type AtlasRepositoryLinkInformationInformation {
   linkType: String
   linkValue: String
 }
@@ -72,7 +74,7 @@ type ParticipantRepoDataTypeSummary {
 type ParticipantRepoDataTypeInformation {
   dataType: String
   count: Long
-  linkInformation: AtlasRepoSummaryLinkInformation
+  linkInformation: AtlasRepositoryLinkInformationInformation
 }
 
 type DataTypeSummaryInformation {

diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java
@@ -34,44 +34,40 @@ public void testConstructor() throws Exception {
 
 		assertEquals("stuff", rowToTest.getOmicsType());
 		assertEquals(expectedLinkInformation, rowToTest.getLinkInformation());
-		assertEquals(0, rowToTest.getOpenCount());
-		assertEquals(0, rowToTest.getControlledCount());
 	}
 
 	@Test
-	public void testSetOpenCount() {
-		row.setOpenCount(43);
+	public void testSetAkiCount() {
+		row.setAkiCount(Long.valueOf(43));
 
-		assertEquals(43, row.getOpenCount());
+		assertEquals(Long.valueOf(43), row.getAkiCount());
 	}
 
 	@Test
-	public void testSetControlledCount() {
-		row.setControlledCount(44);
+	public void testSetCkdCount() {
+		row.setCkdCount(Long.valueOf(44));
 
-		assertEquals(44, row.getControlledCount());
+		assertEquals(Long.valueOf(44), row.getCkdCount());
 	}
 
 	@Test
-	public void testSetOmicsType() {
-		row.setOmicsType("omicsType 2");
-		assertEquals("omicsType 2", row.getOmicsType());
+	public void testSetHrtCount() {
+		row.setHrtCount(Long.valueOf(45));
+
+		assertEquals(Long.valueOf(45), row.getHrtCount());
 	}
 
 	@Test
-	public void testAddToControlledCount() {
-		row.setControlledCount(2);
-		row.addToControlledCount(30);
+	public void testSetDmrCount() {
+		row.setDmrCount(Long.valueOf(46));
 
-		assertEquals(32, row.getControlledCount());
+		assertEquals(Long.valueOf(46), row.getDmrCount());
 	}
 
 	@Test
-	public void testAddToOpenCount() {
-		row.setOpenCount(5);
-		row.addToOpenCount(5);
-
-		assertEquals(10, row.getOpenCount());
+	public void testSetOmicsType() {
+		row.setOmicsType("omicsType 2");
+		assertEquals("omicsType 2", row.getOmicsType());
 	}
 
 	@Test

diff --git a/.../AtlasRepoSummaryLinkInformationTest.java → ...y/AtlasRepositoryLinkInformationTest.java b/.../AtlasRepoSummaryLinkInformationTest.java → ...y/AtlasRepositoryLinkInformationTest.java
@@ -6,7 +6,7 @@
 import org.junit.Before;
 import org.junit.Test;
 
-public class AtlasRepoSummaryLinkInformationTest {
+public class AtlasRepositoryLinkInformationTest {
 
 	@Before
 	public void setUp() throws Exception {

diff --git a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java
@@ -5,6 +5,7 @@
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.ArrayList;
 
 import org.junit.After;
 import org.junit.Before;
@@ -43,63 +44,93 @@ public void tearDown() throws Exception {
 
 	@Test
 	public void testGetAtlasRepoSummary() throws Exception {
-		ExperimentalStrategyValue clinicalData = new ExperimentalStrategyValue();
-		clinicalData.setDataCategory("stuff");
-		clinicalData.setExperimentalStrategy("");
-		clinicalData.setDataType("Clinical Study Data");
-		clinicalData.setCount(1);
-		clinicalData.setAccess("open");
-		ExperimentalStrategyValue biomarker1 = new ExperimentalStrategyValue();
-		biomarker1.setDataCategory("Biomarker");
-		biomarker1.setExperimentalStrategy("something");
-		biomarker1.setDataType("stuff");
-		biomarker1.setDataCategory("Biomarker");
-		biomarker1.setCount(5);
-		biomarker1.setAccess("open");
-		ExperimentalStrategyValue biomarker2 = new ExperimentalStrategyValue();
-		biomarker2.setDataCategory("Biomarker");
-		biomarker2.setDataType("more stuff");
-		biomarker2.setExperimentalStrategy("something else");
-		biomarker2.setDataCategory("Biomarker");
-		biomarker2.setCount(10);
-		biomarker2.setAccess("open");
-		ExperimentalStrategyValue other1 = new ExperimentalStrategyValue();
-		other1.setDataCategory("data category");
-		other1.setDataType("different stuff");
-		other1.setExperimentalStrategy("strategy1");
-		other1.setCount(10);
-		other1.setAccess("open");
-		ExperimentalStrategyValue other2 = new ExperimentalStrategyValue();
-		other2.setDataCategory("data category2");
-		other2.setDataType("even more different stuff");
-		other2.setExperimentalStrategy("strategy1");
-		other2.setCount(10);
-		other2.setAccess("controlled");
-		List<ExperimentalStrategyValue> strategyValues = Arrays.asList(clinicalData, biomarker1, biomarker2, other1,
-				other2);
-		when(atlasRepoSummaryRepository.findAll()).thenReturn(strategyValues);
-		when(fileInfoService.getRepositoryTotalFileCount()).thenReturn(36l);
-
-		AtlasRepoSummaryResult result = dataSummaryService.getAtlasRepoSummary();
-		List<AtlasRepoSummaryRow> summaryRows = result.getSummaryRows();
-		assertEquals(3, summaryRows.size());
-		assertEquals("Biomarkers", summaryRows.get(0).getOmicsType());
-		assertEquals(0, summaryRows.get(0).getControlledCount());
-		assertEquals(15, summaryRows.get(0).getOpenCount());
-		assertEquals(new AtlasRepositoryLinkInformation("data_category", "Biomarker"),
-				summaryRows.get(0).getLinkInformation());
-		assertEquals("Clinical Study Data", summaryRows.get(1).getOmicsType());
-		assertEquals(0, summaryRows.get(1).getControlledCount());
-		assertEquals(1, summaryRows.get(1).getOpenCount());
-		assertEquals(new AtlasRepositoryLinkInformation("data_category", "stuff"),
-				summaryRows.get(1).getLinkInformation());
-		assertEquals("strategy1", summaryRows.get(2).getOmicsType());
-		assertEquals(10, summaryRows.get(2).getControlledCount());
-		assertEquals(10, summaryRows.get(2).getOpenCount());
-		assertEquals(new AtlasRepositoryLinkInformation("experimental_strategy", "strategy1"),
-				summaryRows.get(2).getLinkInformation());
-		assertEquals(Long.valueOf(36), result.getTotalFiles());
+		List<ExperimentalStrategyValue> strategies = new ArrayList<>(
+			Arrays.asList(
+				new ExperimentalStrategyValue(),
+				new ExperimentalStrategyValue(),
+				new ExperimentalStrategyValue(),
+				new ExperimentalStrategyValue()
+			)
+		);
 
+		strategies.get(0).setExperimentalStrategy("abcd");
+		strategies.get(0).setDataCategory("Biomarker");
+		strategies.get(0).setDataType("datatype");
+
+		strategies.get(1).setExperimentalStrategy("");
+		strategies.get(1).setDataCategory("category");
+		strategies.get(1).setDataType("Clinical Study Data");
+
+		strategies.get(2).setExperimentalStrategy("strategy1");
+		strategies.get(2).setDataCategory("category1");
+		strategies.get(2).setDataType("datatype");
+
+		strategies.get(3).setExperimentalStrategy("strategy2");
+		strategies.get(3).setDataCategory("category2");
+		strategies.get(3).setDataType("datatype");
+
+		when(atlasRepoSummaryRepository.findAll()).thenReturn(strategies);
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
+				"abcd")).thenReturn(Long.valueOf(1));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(),
+				"abcd")).thenReturn(Long.valueOf(2));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(),
+				"abcd")).thenReturn(Long.valueOf(3));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
+				"abcd")).thenReturn(4l);
+
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
+				"")).thenReturn(Long.valueOf(5));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(),
+				"")).thenReturn(Long.valueOf(6));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(),
+				"")).thenReturn(Long.valueOf(7));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
+				"")).thenReturn(8l);
+
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
+				"strategy1")).thenReturn(Long.valueOf(9));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(),
+				"strategy1")).thenReturn(Long.valueOf(10));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(),
+				"strategy1")).thenReturn(Long.valueOf(11));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
+				"strategy1")).thenReturn(12l);
+
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(),
+				"strategy2")).thenReturn(Long.valueOf(13));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(),
+				"strategy2")).thenReturn(Long.valueOf(14));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(),
+				"strategy2")).thenReturn(Long.valueOf(15));
+		when(dataSummaryRepository.getRepoDataSummaryCount(TissueTypeEnum.DMR.getParticipantTissueType(),
+				"strategy2")).thenReturn(16l);
+
+		List<AtlasRepoSummaryRow> result = dataSummaryService.getAtlasRepoSummary().getSummaryRows();
+
+		assertEquals("Biomarkers", result.get(0).getOmicsType());
+		assertEquals(Long.valueOf(1), result.get(0).getAkiCount());
+		assertEquals(Long.valueOf(2), result.get(0).getCkdCount());
+		assertEquals(Long.valueOf(3), result.get(0).getHrtCount());
+		assertEquals(Long.valueOf(4), result.get(0).getDmrCount());
+
+		assertEquals("Clinical Study Data", result.get(1).getOmicsType());
+		assertEquals(Long.valueOf(5), result.get(1).getAkiCount());
+		assertEquals(Long.valueOf(6), result.get(1).getCkdCount());
+		assertEquals(Long.valueOf(7), result.get(1).getHrtCount());
+		assertEquals(Long.valueOf(8), result.get(1).getDmrCount());
+
+		assertEquals("strategy1", result.get(2).getOmicsType());
+		assertEquals(Long.valueOf(9), result.get(2).getAkiCount());
+		assertEquals(Long.valueOf(10), result.get(2).getCkdCount());
+		assertEquals(Long.valueOf(11), result.get(2).getHrtCount());
+		assertEquals(Long.valueOf(12), result.get(2).getDmrCount());
+
+		assertEquals("strategy2", result.get(3).getOmicsType());
+		assertEquals(Long.valueOf(13), result.get(3).getAkiCount());
+		assertEquals(Long.valueOf(14), result.get(3).getCkdCount());
+		assertEquals(Long.valueOf(15), result.get(3).getHrtCount());
+		assertEquals(Long.valueOf(16), result.get(3).getDmrCount());
 	}
 
 	@Test