implement backend for participant Clincial

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

@@ -18,6 +18,7 @@
 import org.kpmp.geneExpression.*;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummary;
 import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService;
+import org.kpmp.participant.ParticipantClinicalDataset;
 import org.kpmp.participant.ParticipantDataTypeSummary;
 import org.kpmp.participant.ParticipantRepoDataTypeInformation;
 import org.kpmp.participant.ParticipantRepoDataTypeSummary;
@@ -191,6 +192,16 @@ public List<RPAccessionGroup> getRPGeneExpressionByTissue(@Argument String geneS
 		}
 	}
 
+    @QueryMapping
+    public ParticipantClinicalDataset getParticipantClinicalDataset(@Argument String redcapId) {
+        try{
+            return participantService.getParticipantClinicalDataset(redcapId);
+        }catch (Exception e) {
+            logger.error(e.getMessage());
+            throw e;
+        }
+    }
+
     @QueryMapping
 	public ParticipantDataTypeSummary getDataTypeInformationByParticipant(@Argument String redcapId) {
 		return participantService.getExperimentCounts(redcapId);

src/main/java/org/kpmp/participant/ParticipantClinicalDataset.java

@@ -0,0 +1,147 @@
+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 = "participant_clinical")
+public class ParticipantClinicalDataset implements Serializable{
+    @Id
+    @Column(name="participant_clinical_id")
+    private int participantClinicalId;
+    @Column(unique = true, name = "participant_id")
+    private int participantId;
+    @Column(name = "kdigo_stage")
+    private String kdigoStage;
+    @Column(name = "baseline_egfr")
+    private String baselineEgfr;
+    @Column(name = "proteinuria")
+    private String proteinuria;
+    @Column(name = "a1c")
+    private String a1c;
+    @Column(name = "albuminuria")
+    private String albuminuria;
+    @Column(name = "diabetes_history")
+    private String diabetesHistory;
+    @Column(name = "diabetes_duration")
+    private String diabetesDuration;
+    @Column(name = "hypertension_history")
+    private String hypertensionHistory;
+    @Column(name = "hypertension_duration")
+    private String hypertensionDuration;
+    @Column(name = "on_raas_blockade")
+    private String onRaasBlockade;
+    @Column(name = "race")
+    private String race;
+
+
+    public int getParticipantClinicalId() {
+        return this.participantClinicalId;
+    }
+
+    public void setParticipantClinicalId(int participantClinicalId) {
+        this.participantClinicalId = participantClinicalId;
+    }
+
+    public int getParticipantId() {
+        return this.participantId;
+    }
+
+    public void setParticipantId(int participantId) {
+        this.participantId = participantId;
+    }
+
+    public String getKdigoStage() {
+        return this.kdigoStage;
+    }
+
+    public void setKdigoStage(String kdigoStage) {
+        this.kdigoStage = kdigoStage;
+    }
+
+    public String getBaselineEgfr() {
+        return this.baselineEgfr;
+    }
+
+    public void setBaselineEgfr(String baselineEgfr) {
+        this.baselineEgfr = baselineEgfr;
+    }
+
+    public String getProteinuria() {
+        return this.proteinuria;
+    }
+
+    public void setProteinuria(String proteinuria) {
+        this.proteinuria = proteinuria;
+    }
+
+    public String getA1c() {
+        return this.a1c;
+    }
+
+    public void setA1c(String a1c) {
+        this.a1c = a1c;
+    }
+
+    public String getAlbuminuria() {
+        return this.albuminuria;
+    }
+
+    public void setAlbuminuria(String albuminuria) {
+        this.albuminuria = albuminuria;
+    }
+
+    public String getDiabetesHistory() {
+        return this.diabetesHistory;
+    }
+
+    public void setDiabetesHistory(String diabetesHistory) {
+        this.diabetesHistory = diabetesHistory;
+    }
+
+    public String getDiabetesDuration() {
+        return this.diabetesDuration;
+    }
+
+    public void setDiabetesDuration(String diabetesDuration) {
+        this.diabetesDuration = diabetesDuration;
+    }
+
+    public String getHypertensionHistory() {
+        return this.hypertensionHistory;
+    }
+
+    public void setHypertensionHistory(String hypertensionHistory) {
+        this.hypertensionHistory = hypertensionHistory;
+    }
+
+    public String getHypertensionDuration() {
+        return this.hypertensionDuration;
+    }
+
+    public void setHypertensionDuration(String hypertensionDuration) {
+        this.hypertensionDuration = hypertensionDuration;
+    }
+
+    public String getOnRaasBlockade() {
+        return this.onRaasBlockade;
+    }
+
+    public void setOnRaasBlockade(String onRaasBlockade) {
+        this.onRaasBlockade = onRaasBlockade;
+    }
+
+    public void setRace(String race){
+        this.race = race;
+    }
+
+    public String getRace() {
+        return race;
+    }
+
+}
+

src/main/java/org/kpmp/participant/ParticipantClinicalDatasetRepository.java

@@ -0,0 +1,15 @@
+package org.kpmp.participant;
+
+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 ParticipantClinicalDatasetRepository extends CrudRepository<ParticipantClinicalDataset, Long> {
+
+	@Cacheable("participantById")
+    @Query(value = "select * from participant_clinical where participant_id= :participantId", nativeQuery = true)
+	ParticipantClinicalDataset findByParticipantId(@Param("participantId") Integer participantId);
+}

src/main/java/org/kpmp/participant/ParticipantService.java

@@ -41,13 +41,14 @@ public class ParticipantService {
 	private RTParticipantRepository rtParticipantRepo;
 	private ParticipantRepoDataRepository fileByParticipantRepo;
 	private RPParticipantRepository rpParticipantRepository;
+    private ParticipantClinicalDatasetRepository participantClinicalDatasetRepo;
 
 	@Autowired
 	public ParticipantService(DataSummaryRepository dataSummaryRepo, SpatialViewerTypeRepository svTypeRepo,
 			SingleCellMetadataRepository scMetadataRepo, SingleNucleusMetadataRepository snMetadataRepo,
 			RTParticipantRepository rtParticipantRepo,
 			ParticipantSummaryDatasetRepository participantSummaryDatasetRepository, RPParticipantRepository rpParticipantRepository,
-			ParticipantRepoDataRepository fileByParticipantRepo) {
+			ParticipantRepoDataRepository fileByParticipantRepo, ParticipantClinicalDatasetRepository participantClinicalDatasetRepo) {
 		this.dataSummaryRepo = dataSummaryRepo;
 		this.svTypeRepo = svTypeRepo;
 		this.scMetadataRepo = scMetadataRepo;
@@ -56,8 +57,14 @@ public ParticipantService(DataSummaryRepository dataSummaryRepo, SpatialViewerTy
 		this.participantSummaryDatasetRepository = participantSummaryDatasetRepository;
 		this.rpParticipantRepository = rpParticipantRepository;
 		this.fileByParticipantRepo = fileByParticipantRepo;
+        this.participantClinicalDatasetRepo = participantClinicalDatasetRepo; 
 	}
 
+    public ParticipantClinicalDataset getParticipantClinicalDataset(String redcapId){
+        Integer participantId = participantSummaryDatasetRepository.findIdByRedcapId(redcapId);
+        return participantClinicalDatasetRepo.findByParticipantId(participantId);
+    }
+
 	public ParticipantSummaryDataset getParticipantSummaryDataset(String redcapId) {
 		return participantSummaryDatasetRepository.findByRedcapId(redcapId);
 	}

src/main/java/org/kpmp/participant/ParticipantSummaryDatasetRepository.java

@@ -13,6 +13,9 @@ public interface ParticipantSummaryDatasetRepository extends CrudRepository<Part
     @Query(value = "select * from participant where redcap_id= :redcapId", nativeQuery = true)
 	ParticipantSummaryDataset findByRedcapId(@Param("redcapId") String redcapId);
 
+    @Query(value = "SELECT participant_id FROM participant WHERE redcap_id= :redcapId", nativeQuery = true)
+    Integer findIdByRedcapId(@Param("redcapId") String redcapId);
+
 	@Cacheable("partipantByEnrollmentCategory")
 	@Query(value = "select count(*) from participant where enrollment_category= :enrollment_category", nativeQuery = true)
 	Long getDataSummaryCount(@Param("enrollment_category") String enrollment_category);

src/main/resources/graphql/knowledge_environment.graphqls

@@ -20,6 +20,7 @@ type Query {
   getAtlasSummaryRows: AtlasRepoSummaryResult
   getAtlasMessages: [AtlasMessages]
   getExperimentalStrategyCountsByParticipant(redcapId: String!): [ParticipantRepoDataTypeInformation]
+  getParticipantClinicalDataset(redcapId: String!): ParticipantClinicalDataset
 }
 
 type AtlasMessages {
@@ -220,4 +221,20 @@ type ParticipantSummaryDataset {
   redcapId: String
   enrollmentCategory: String
   clinicalData: String
+}
+
+type ParticipantClinicalDataset {
+    participantId: String
+    participantClinicalId: String
+    kdigoStage: String
+    baselineEgfr: String
+    proteinuria: String
+    a1c: String
+    albuminuria: String
+    diabetesHistory: String
+    diabetesDuration: String
+    hypertensionHistory: String
+    hypertensionDuration: String
+    onRaasBlockade: String
+    race: String
 }

src/test/java/org/kpmp/QueryControllerTest.java

@@ -37,6 +37,7 @@
 import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService;
 import org.kpmp.geneExpressionSummary.singleCell.SCRNAGeneExpressionExpressionSummaryValue;
 import org.kpmp.geneExpressionSummary.singleNucleus.SNRNAGeneExpressionExpressionSummaryValue;
+import org.kpmp.participant.ParticipantClinicalDataset;
 import org.kpmp.participant.ParticipantDataTypeSummary;
 import org.kpmp.participant.ParticipantRepoDataTypeInformation;
 import org.kpmp.participant.ParticipantRepoDataTypeSummary;
@@ -283,6 +284,16 @@ public void testGetRepoDataTypeInformationByParticipant() throws Exception {
 
 	}
 
+    @Test
+    public void testGetParticipantClincialDataset() throws Exception {
+        ParticipantClinicalDataset expected = new ParticipantClinicalDataset();
+		when(participantService.getParticipantClinicalDataset("participant_id")).thenReturn(expected);
+
+		assertEquals(expected, query.getParticipantClinicalDataset("participant_id"));
+		verify(participantService).getParticipantClinicalDataset("participant_id");
+    }
+
+    @Test
 	public void testParticipantSummaryDataset() throws Exception {
 		ParticipantSummaryDataset expected = new ParticipantSummaryDataset();
 		when(participantService.getParticipantSummaryDataset("participant_id")).thenReturn(expected);
@@ -291,6 +302,7 @@ public void testParticipantSummaryDataset() throws Exception {
 		verify(participantService).getParticipantSummaryDataset("participant_id");
 	}
 
+    @Test
 	public void getParticipantEnrollmentCategorySummary() throws Exception {
 		List<ParticipantEnrollmentCategorySummary> expectedResult = new ArrayList<>();
 

src/test/java/org/kpmp/participant/ParticipantClinicalDatasetTest.java

@@ -0,0 +1,102 @@
+package org.kpmp.participant;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestInstance.Lifecycle;
+
+@TestInstance(Lifecycle.PER_CLASS)
+public class ParticipantClinicalDatasetTest {
+    ParticipantClinicalDataset participantClinicalDataset;
+
+    @BeforeAll
+    public void setUp() throws Exception {
+        this.participantClinicalDataset = new ParticipantClinicalDataset();
+    }
+
+    @AfterAll
+    public void tearDown() throws Exception {
+        participantClinicalDataset = null;
+    }
+
+    @Test
+    void testSetParticipantClicalId() {
+        participantClinicalDataset.setParticipantClinicalId(0);
+        assertEquals(0, participantClinicalDataset.getParticipantClinicalId());
+    }
+
+    @Test
+    void testSetParticipantId() {
+        participantClinicalDataset.setParticipantId(2);
+        assertEquals(2, participantClinicalDataset.getParticipantId());
+    }
+
+    @Test
+    void testSetKdigoStage() {
+        participantClinicalDataset.setKdigoStage("Stage 1");
+        assertEquals("Stage 1", participantClinicalDataset.getKdigoStage());
+    }
+
+    @Test
+    void testSetBaselineEgfr() {
+        participantClinicalDataset.setBaselineEgfr("blah");
+        assertEquals("blah", participantClinicalDataset.getBaselineEgfr());
+    }
+
+    @Test
+    void testSetProteinuria() {
+        participantClinicalDataset.setProteinuria("proteinuria");
+        assertEquals("proteinuria", participantClinicalDataset.getProteinuria());
+    }
+
+    @Test
+    void testSetA1c() {
+        participantClinicalDataset.setA1c("a1c");
+        assertEquals("a1c", participantClinicalDataset.getA1c());
+    }
+
+    @Test
+    void testSetAlbuminuria() {
+        participantClinicalDataset.setAlbuminuria("ouchie");
+        assertEquals("ouchie", participantClinicalDataset.getAlbuminuria());
+    }
+
+    @Test
+    void testSetDiabetesHistory() {
+        participantClinicalDataset.setDiabetesHistory("nope");
+        assertEquals("nope", participantClinicalDataset.getDiabetesHistory());
+    }
+
+    @Test
+    void testSetDiabetesDuration () {
+        participantClinicalDataset.setDiabetesDuration("since the stone age");
+        assertEquals("since the stone age", participantClinicalDataset.getDiabetesDuration());
+    }
+
+    @Test
+    void testSetHypertensionHistory() {
+        participantClinicalDataset.setHypertensionHistory("yes");
+        assertEquals("yes", participantClinicalDataset.getHypertensionHistory());
+    }
+
+    @Test
+    void testSetHypertensionDuration() {
+        participantClinicalDataset.setHypertensionDuration("since the bronze age");
+        assertEquals("since the bronze age", participantClinicalDataset.getHypertensionDuration());
+    }
+
+    @Test
+    void testSetOnRaasBlockade() {
+        participantClinicalDataset.setOnRaasBlockade("yes");
+        assertEquals("yes", participantClinicalDataset.getOnRaasBlockade());
+    }
+
+    @Test
+    void testSetRace(){
+        participantClinicalDataset.setRace("alien from outer space");
+        assertEquals("alien from outer space", participantClinicalDataset.getRace());
+    }
+
+}