Merge pull request #154 from KPMP/KPMP-5366_fix_graphql_endpoints

KPMP-5366: update endpoints, remove clinicalData from participant summary
KPMP · Nov 11, 2024 · 8973644 · 8973644
2 parents e3694ff + db0a720
commit 8973644
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Showing 9 changed files with 21 additions and 40 deletions.
diff --git a/src/main/java/org/kpmp/QueryController.java b/src/main/java/org/kpmp/QueryController.java
@@ -141,7 +141,7 @@ public List<String> dataTypesForConcept(@Argument String geneSymbol, @Argument S
 	}
 
     @QueryMapping
-	public RTExpressionByEnrollmentCategory getRTGeneExpressionByTissue(@Argument String comparisonType, @Argument String geneSymbol)
+	public RTExpressionByEnrollmentCategory getRTGeneExpressionByEnrollment(@Argument String comparisonType, @Argument String geneSymbol)
 			throws Exception {
 		try {
 			return rtExpressionDataService.getByComparisonTypeAndGeneSymbolPerEnrollment(comparisonType, geneSymbol);
@@ -152,9 +152,9 @@ public RTExpressionByEnrollmentCategory getRTGeneExpressionByTissue(@Argument St
 	}
 
     @QueryMapping
-	public RPExpressionByEnrollmentCategory getRPGeneExpressionByTissueAndProtein(@Argument String geneSymbol, @Argument String protein) throws Exception {
+	public RPExpressionByEnrollmentCategory getRPGeneExpressionByEnrollmentAndProtein(@Argument String geneSymbol, @Argument String protein) throws Exception {
 		try {
-			return rpExpressionDataService.getByGeneSymbolAndProteinPerTissue(geneSymbol, protein);
+			return rpExpressionDataService.getByGeneSymbolAndProteinPerEnrollment(geneSymbol, protein);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;
@@ -182,10 +182,10 @@ public List<RPExpressionData> getRPGeneExpressionByStructure(@Argument String st
 	}
 
     @QueryMapping
-	public List<RPAccessionGroup> getRPGeneExpressionByTissue(@Argument String geneSymbol)
+	public List<RPAccessionGroup> getRPGeneExpressionByEnrollment(@Argument String geneSymbol)
 			throws Exception {
 		try {
-			return rpExpressionDataService.getByGeneSymbolPerTissue(geneSymbol);
+			return rpExpressionDataService.getByGeneSymbolPerEnrollment(geneSymbol);
 		} catch (Exception e) {
 			logger.error(e.getMessage());
 			throw e;

diff --git a/src/main/java/org/kpmp/geneExpression/RPExpressionDataService.java b/src/main/java/org/kpmp/geneExpression/RPExpressionDataService.java
@@ -17,18 +17,18 @@ public RPExpressionDataService(RPExpressionDataRepository rpExpressionDataReposi
         this.rpExpressionDataRepository = rpExpressionDataRepository;
     }
 
-    public List<RPAccessionGroup> getByGeneSymbolPerTissue(String geneSymbol) {
+    public List<RPAccessionGroup> getByGeneSymbolPerEnrollment(String geneSymbol) {
         List<String> accessionNums = rpExpressionDataRepository.findAccessionByGeneSymbol(geneSymbol);
         List<RPAccessionGroup> groups = new ArrayList<>();
         for (String accession: accessionNums) {
-            RPExpressionByEnrollmentCategory rpExpressionByEnrollmentCategory = getByGeneSymbolAndProteinPerTissue(geneSymbol, accession);
+            RPExpressionByEnrollmentCategory rpExpressionByEnrollmentCategory = getByGeneSymbolAndProteinPerEnrollment(geneSymbol, accession);
             RPAccessionGroup group = new RPAccessionGroup(accession, rpExpressionByEnrollmentCategory);
             groups.add(group);
         }
         return groups;
     }
 
-    public RPExpressionByEnrollmentCategory getByGeneSymbolAndProteinPerTissue(String geneSymbol, String protein) {
+    public RPExpressionByEnrollmentCategory getByGeneSymbolAndProteinPerEnrollment(String geneSymbol, String protein) {
         RPExpressionByEnrollmentCategory rpExpressionByEnrollmentCategory = new RPExpressionByEnrollmentCategory();
 
         rpExpressionByEnrollmentCategory.setAll(rpExpressionDataRepository.findByGeneSymbolAndEnrollmentCategoryAndProteinWithCounts(geneSymbol, EnrollmentCategoryEnum.ALL.getParticipantEnrollmentCategory(), protein));

diff --git a/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java b/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java
@@ -28,8 +28,6 @@ public class ParticipantSummaryDataset implements Serializable {
 	private String sampleType;
 	@Column(name = "enrollment_category")
 	private String enrollmentCategory;
-	@Column(name = "clinical_data")
-	private String clinicalData;
 
 	public int getParticipantId() {
 		return participantId;
@@ -103,12 +101,4 @@ public void setEnrollmentCategory(String enrollmentCategory) {
 		this.enrollmentCategory = enrollmentCategory;
 	}
 
-	public String getClinicalData() {
-		return clinicalData;
-	}
-
-	public void setClinicalData(String clinicalData) {
-		this.clinicalData = clinicalData;
-	}
-
 }
diff --git a/src/main/resources/graphql/knowledge_environment.graphqls b/src/main/resources/graphql/knowledge_environment.graphqls
@@ -220,7 +220,6 @@ type ParticipantSummaryDataset {
   participantId: String
   redcapId: String
   enrollmentCategory: String
-  clinicalData: String
 }
 
 type ParticipantClinicalDataset {

diff --git a/src/test/java/org/kpmp/QueryControllerTest.java b/src/test/java/org/kpmp/QueryControllerTest.java
@@ -240,7 +240,7 @@ public void testGetRTGeneExpression() throws Exception {
 		rtExpressionByEnrollmentCategory.setAki(data);
 		when(rtExpressionDataService.getByComparisonTypeAndGeneSymbolPerEnrollment("all_segments", "gene"))
 				.thenReturn(rtExpressionByEnrollmentCategory);
-		assertEquals(rtExpressionByEnrollmentCategory, query.getRTGeneExpressionByTissue("all_segments", "gene"));
+		assertEquals(rtExpressionByEnrollmentCategory, query.getRTGeneExpressionByEnrollment("all_segments", "gene"));
 		assertEquals(rtExpressionByEnrollmentCategory.getAki(), data);
 	}
 
@@ -253,11 +253,11 @@ public void testGetRTGeneExpressionByStructure() throws Exception {
 	}
 
 	@Test
-	public void testGetRPGeneExpressionByTissueAndProtein() throws Exception {
+	public void testGetRPGeneExpressionByEnrollmentAndProtein() throws Exception {
 		RPExpressionByEnrollmentCategory expected = new RPExpressionByEnrollmentCategory();
-		when(rpExpressionDataService.getByGeneSymbolAndProteinPerTissue("APOL1", "steak")).thenReturn(expected);
+		when(rpExpressionDataService.getByGeneSymbolAndProteinPerEnrollment("APOL1", "steak")).thenReturn(expected);
 
-		RPExpressionByEnrollmentCategory result = query.getRPGeneExpressionByTissueAndProtein("APOL1", "steak");
+		RPExpressionByEnrollmentCategory result = query.getRPGeneExpressionByEnrollmentAndProtein("APOL1", "steak");
 
 		assertEquals(expected, result);
 	}

diff --git a/src/test/java/org/kpmp/geneExpression/RPExpressionDataServiceTest.java b/src/test/java/org/kpmp/geneExpression/RPExpressionDataServiceTest.java
@@ -35,7 +35,7 @@ public void tearDown() throws Exception {
     }
 
     @Test
-    public void testGetByGeneSymbolPerTissue() throws Exception {
+    public void testGetByGeneSymbolPerEnrollment() throws Exception {
 
         List<String> accessions = new ArrayList<>();
         accessions.add("a1");
@@ -52,7 +52,7 @@ public void testGetByGeneSymbolPerTissue() throws Exception {
         when(rpExpressionDataRepository.findByGeneSymbolAndEnrollmentCategoryAndProteinWithCounts("gene", EnrollmentCategoryEnum.ALL.getParticipantEnrollmentCategory(), "a2")).
                 thenReturn(rpExpressionDataAll2);
 
-        List<RPAccessionGroup> rpAccessionGroups = rpExpressionDataService.getByGeneSymbolPerTissue("gene");
+        List<RPAccessionGroup> rpAccessionGroups = rpExpressionDataService.getByGeneSymbolPerEnrollment("gene");
 
         assertEquals("a1", rpAccessionGroups.get(0).getAccession());
         assertEquals("a2", rpAccessionGroups.get(1).getAccession());
@@ -66,13 +66,13 @@ public void testGetByGeneSymbolPerTissue() throws Exception {
     }
 
     @Test
-    public void testGetByGeneSymbolAndProteinPerTissue() throws Exception {
+    public void testgetByGeneSymbolAndProteinPerEnrollment() throws Exception {
         List<RPExpressionData>  rpExpressionDataAll = Arrays.asList(new RPExpressionData[]{new RPExpressionData()});
 
         when(rpExpressionDataRepository.findByGeneSymbolAndEnrollmentCategoryAndProteinWithCounts("gene", EnrollmentCategoryEnum.ALL.getParticipantEnrollmentCategory(), "protein")).
                 thenReturn(rpExpressionDataAll);
 
-        RPExpressionByEnrollmentCategory rpExpressionByEnrollmentCategory = rpExpressionDataService.getByGeneSymbolAndProteinPerTissue("gene", "protein");
+        RPExpressionByEnrollmentCategory rpExpressionByEnrollmentCategory = rpExpressionDataService.getByGeneSymbolAndProteinPerEnrollment("gene", "protein");
 
         assertEquals(rpExpressionByEnrollmentCategory.getAll(), rpExpressionDataAll);
     }

diff --git a/src/test/java/org/kpmp/geneExpression/RTExpressionDataServiceTest.java b/src/test/java/org/kpmp/geneExpression/RTExpressionDataServiceTest.java
@@ -35,7 +35,7 @@ public void tearDown() throws Exception {
 	}
 
 	@Test
-	public void testGetByComparisonTypeAndGeneSymbolPerTissue_all() throws Exception {
+	public void testGetByComparisonTypeAndGeneSymbolPerEnrollment_all() throws Exception {
 
 		RTExpressionDataAllSegments allallData = new RTExpressionDataAllSegments();
 		List<RTExpressionDataAllSegments> allallDataList = Arrays.asList(allallData);
@@ -58,7 +58,7 @@ public void testGetByComparisonTypeAndGeneSymbolPerTissue_all() throws Exception
 	}
 
 	@Test
-	public void testGetByComparisonTypeAndGeneSymbolPerTissue_hrt() throws Exception {
+	public void testGetByComparisonTypeAndGeneSymbolPerEnrollment_hrt() throws Exception {
 
 		RTExpressionDataAllSegments allhrtData = new RTExpressionDataAllSegments();
 		List<RTExpressionDataAllSegments> allhrtDataList = Arrays.asList(allhrtData);
@@ -81,7 +81,7 @@ public void testGetByComparisonTypeAndGeneSymbolPerTissue_hrt() throws Exception
 	}
 
 	@Test
-	public void testGetByComparisonTypeAndGeneSymbolPerTissue_ckd() throws Exception {
+	public void testGetByComparisonTypeAndGeneSymbolPerEnrollment_ckd() throws Exception {
 		RTExpressionDataAllSegments allckdData = new RTExpressionDataAllSegments();
 		List<RTExpressionDataAllSegments> allckdDataList = Arrays.asList(allckdData);
 		RTExpressionDataGTI gckdData = new RTExpressionDataGTI();
@@ -103,7 +103,7 @@ public void testGetByComparisonTypeAndGeneSymbolPerTissue_ckd() throws Exception
 	}
 
 	@Test
-	public void testGetByComparisonTypeAndGeneSymbolPerTissue_aki() throws Exception {
+	public void testGetByComparisonTypeAndGeneSymbolPerEnrollment_aki() throws Exception {
 		RTExpressionDataAllSegments allAkiData = new RTExpressionDataAllSegments();
 		List<RTExpressionDataAllSegments> allAkiDataList = Arrays.asList(allAkiData);
 		RTExpressionDataGTI gAkiData = new RTExpressionDataGTI();
@@ -125,7 +125,7 @@ public void testGetByComparisonTypeAndGeneSymbolPerTissue_aki() throws Exception
 	}
 
 	@Test
-	public void testGetByComparisonTypeAndGeneSymbolPerTissue_dmr() throws Exception {
+	public void testGetByComparisonTypeAndGeneSymbolPerEnrollment_dmr() throws Exception {
 		RTExpressionDataAllSegments allDmrData = new RTExpressionDataAllSegments();
 		List<RTExpressionDataAllSegments> allDmrDataList = Arrays.asList(allDmrData);
 		RTExpressionDataGTI gDmrData = new RTExpressionDataGTI();

diff --git a/src/test/java/org/kpmp/participant/ParticipantServiceTest.java b/src/test/java/org/kpmp/participant/ParticipantServiceTest.java
@@ -118,7 +118,6 @@ public void testGetParticipantSummaryDataset() throws Exception {
 		expectedResult.setProtocol("7");
 		expectedResult.setSampleType("8");
 		expectedResult.setEnrollmentCategory("9");
-		expectedResult.setClinicalData("10");
 
 		when(participantSummaryDatasetRepository.findByRedcapId("1")).thenReturn(expectedResult);
 
@@ -135,7 +134,6 @@ public void testGetParticipantSummaryDataset() throws Exception {
 		assertEquals("7", result.getProtocol());
 		assertEquals("8", result.getSampleType());
 		assertEquals("9", result.getEnrollmentCategory());
-		assertEquals("10", result.getClinicalData());
 	}
 
 	@Test

diff --git a/src/test/java/org/kpmp/participant/ParticipantSummaryDatasetTest.java b/src/test/java/org/kpmp/participant/ParticipantSummaryDatasetTest.java
@@ -76,10 +76,4 @@ void setEnrollmentCategory() {
         assertEquals("tissue", participantSummaryDataset.getEnrollmentCategory());
     }
 
-    @Test
-    void setClinicalData() {
-        participantSummaryDataset.setClinicalData("clinical");
-        assertEquals("clinical", participantSummaryDataset.getClinicalData());
-    }
-
 }