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Kpmp 6335 fix dupes #206

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Merged
rlreamy merged 3 commits into from
Mar 5, 2026
Merged

Kpmp 6335 fix dupes #206

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04495a8
KPMP-6335: add id class
zwright Mar 3, 2026
fe34d67
KPMP-6335: add tests
zwright Mar 4, 2026
c45dcfa
KPMP-6335: fix repo id
zwright Mar 4, 2026
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296 changes: 148 additions & 148 deletions src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java
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Original file line number Diff line number Diff line change
@@ -1,148 +1,148 @@
package org.kpmp.geneExpression;
import java.io.Serializable;
import jakarta.persistence.Column;
import jakarta.persistence.Entity;
import jakarta.persistence.Id;
import jakarta.persistence.Table;
@Entity
@Table(name = "rt_segments")
public class RTExpressionDataAllSegments implements RTExpressionData, Serializable {
private static final long serialVersionUID = 9029734049386312455L;
@Id
@Column(name = "id")
private Integer id;
@Column(name = "gene_symbol")
private String geneSymbol;
@Column(name = "segment")
private String segment;
@Column(name = "segment_name")
private String segmentName;
@Column(name = "fold_change")
private Double foldChange;
@Column(name = "p_val")
private Double pVal;
@Column(name = "std_dev")
private Double stdDev;
@Column(name = "p_val_log10")
private Double pValLog10;
@Column(name = "enrollment_category")
private String enrollmentCategory;
@Column(name = "adj_p_val")
private Double adjPVal;
@Column(name = "sample_count")
private Integer sampleCount;
@Override
public Integer getId() {
return id;
}
@Override
public void setId(Integer id) {
this.id = id;
}
@Override
public String getGeneSymbol() {
return geneSymbol;
}
@Override
public void setGeneSymbol(String geneSymbol) {
this.geneSymbol = geneSymbol;
}
@Override
public String getSegment() {
return segment;
}
@Override
public void setSegment(String segment) {
this.segment = segment;
}
@Override
public Double getFoldChange() {
return foldChange;
}
@Override
public void setFoldChange(Double foldChange) {
this.foldChange = foldChange;
}
@Override
public Double getPVal() {
return pVal;
}
@Override
public void setPVal(Double pVal) {
this.pVal = pVal;
}
@Override
public Double getStdDev() {
return stdDev;
}
@Override
public void setStdDev(Double stdDev) {
this.stdDev = stdDev;
}
@Override
public Double getPValLog10() {
return pValLog10;
}
@Override
public void setPValLog10(Double pValLog10) {
this.pValLog10 = pValLog10;
}
@Override
public String getEnrollmentCategory() {
return enrollmentCategory;
}
@Override
public void setEnrollmentCategory(String enrollmentCategory) {
this.enrollmentCategory = enrollmentCategory;
}
@Override
public Integer getSampleCount() {
return sampleCount;
}
@Override
public void setSampleCount(Integer sampleCount) {
this.sampleCount = sampleCount;
}
@Override
public String getSegmentName() {
return segmentName;
}
@Override
public void setSegmentName(String segmentName) {
this.segmentName = segmentName;
}
@Override
public Double getAdjPVal() {
return adjPVal;
}
@Override
public void setAdjPVal(Double adjPVal) {
this.adjPVal = adjPVal;
}
}
package org.kpmp.geneExpression;

import java.io.Serializable;

import jakarta.persistence.*;

@Entity
@Table(name = "rt_segments")
@IdClass(RTExpressionDataId.class)
public class RTExpressionDataAllSegments implements RTExpressionData, Serializable {

private static final long serialVersionUID = 9029734049386312455L;
@Id
@Column(name = "id")
private Integer id;
@Id
@Column(name = "gene_symbol")
private String geneSymbol;
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@Column(name = "segment")
private String segment;
@Column(name = "segment_name")
private String segmentName;
@Column(name = "fold_change")
private Double foldChange;
@Id
@Column(name = "p_val")
private Double pVal;
@Column(name = "std_dev")
private Double stdDev;
@Column(name = "p_val_log10")
private Double pValLog10;
@Column(name = "enrollment_category")
private String enrollmentCategory;
@Column(name = "adj_p_val")
private Double adjPVal;
@Column(name = "sample_count")
private Integer sampleCount;

@Override
public Integer getId() {
return id;
}

@Override
public void setId(Integer id) {
this.id = id;
}

@Override
public String getGeneSymbol() {
return geneSymbol;
}

@Override
public void setGeneSymbol(String geneSymbol) {
this.geneSymbol = geneSymbol;
}

@Override
public String getSegment() {
return segment;
}

@Override
public void setSegment(String segment) {
this.segment = segment;
}

@Override
public Double getFoldChange() {
return foldChange;
}

@Override
public void setFoldChange(Double foldChange) {
this.foldChange = foldChange;
}

@Override
public Double getPVal() {
return pVal;
}

@Override
public void setPVal(Double pVal) {
this.pVal = pVal;
}

@Override
public Double getStdDev() {
return stdDev;
}

@Override
public void setStdDev(Double stdDev) {
this.stdDev = stdDev;
}

@Override
public Double getPValLog10() {
return pValLog10;
}

@Override
public void setPValLog10(Double pValLog10) {
this.pValLog10 = pValLog10;
}

@Override
public String getEnrollmentCategory() {
return enrollmentCategory;
}

@Override
public void setEnrollmentCategory(String enrollmentCategory) {
this.enrollmentCategory = enrollmentCategory;
}

@Override
public Integer getSampleCount() {
return sampleCount;
}

@Override
public void setSampleCount(Integer sampleCount) {
this.sampleCount = sampleCount;
}

@Override
public String getSegmentName() {
return segmentName;
}

@Override
public void setSegmentName(String segmentName) {
this.segmentName = segmentName;
}

@Override
public Double getAdjPVal() {
return adjPVal;
}

@Override
public void setAdjPVal(Double adjPVal) {
this.adjPVal = adjPVal;
}
}
2 changes: 1 addition & 1 deletion src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegmentsRepository.java
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Expand Up @@ -9,7 +9,7 @@
import org.springframework.stereotype.Repository;

@Repository
public interface RTExpressionDataAllSegmentsRepository extends CrudRepository<RTExpressionDataAllSegments, Integer> {
public interface RTExpressionDataAllSegmentsRepository extends CrudRepository<RTExpressionDataAllSegments, RTExpressionDataId> {
@Cacheable("rtExpGeneSymbolAndEnrollmentCategoryWithCounts")
@Query(value = "SELECT rts.*, rsv.sample_count, s.segment_name FROM rt_segments rts "
+ "LEFT JOIN rt_summary_v rsv ON rts.segment = rsv.segment AND rts.enrollment_category = rsv.enrollment_category "
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39 changes: 39 additions & 0 deletions src/main/java/org/kpmp/geneExpression/RTExpressionDataId.java
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@@ -0,0 +1,39 @@
package org.kpmp.geneExpression;

import java.io.Serializable;
import java.util.Objects;

public class RTExpressionDataId implements Serializable {

private Integer id;
private String geneSymbol;
private Double pVal;

public RTExpressionDataId() {}

public RTExpressionDataId(Integer id, String geneSymbol, Double pVal) {
this.id = id;
this.geneSymbol = geneSymbol;
this.pVal = pVal;
}

public Integer getId() { return id; }
public void setId(Integer id) { this.id = id; }
public String getGeneSymbol() { return geneSymbol; }
public void setGeneSymbol(String geneSymbol) { this.geneSymbol = geneSymbol; }
public Double getPVal() { return pVal; }
public void setPVal(Double pVal) { this.pVal = pVal; }

@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
RTExpressionDataId that = (RTExpressionDataId) o;
return Objects.equals(id, that.id) && Objects.equals(geneSymbol, that.geneSymbol) && Objects.equals(pVal, that.pVal);
}

@Override
public int hashCode() {
return Objects.hash(id, geneSymbol, pVal);
}
}
46 changes: 46 additions & 0 deletions src/test/java/org/kpmp/geneExpression/RTExpressionDataIdTest.java
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package org.kpmp.geneExpression;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import org.junit.jupiter.api.Test;

class RTExpressionDataIdTest {

@Test
void testGettersAndSetters() {
RTExpressionDataId idData = new RTExpressionDataId();

idData.setId(101);
idData.setGeneSymbol("SOD1");
idData.setPVal(0.05);

assertEquals(101, idData.getId());
assertEquals("SOD1", idData.getGeneSymbol());
assertEquals(0.05, idData.getPVal());
}

@Test
void testConstructor() {
RTExpressionDataId idData = new RTExpressionDataId(202, "GAPDH", 0.001);

assertEquals(202, idData.getId());
assertEquals("GAPDH", idData.getGeneSymbol());
assertEquals(0.001, idData.getPVal());
}

@Test
void testEqualsAndHashCode() {
RTExpressionDataId id1 = new RTExpressionDataId(1, "ALB", 0.01);
RTExpressionDataId id2 = new RTExpressionDataId(1, "ALB", 0.01);
RTExpressionDataId id3 = new RTExpressionDataId(2, "ALB", 0.01);
RTExpressionDataId id4 = new RTExpressionDataId(1, "INS", 0.01);

assertEquals(id1, id2);
assertNotEquals(id1, id3);
assertNotEquals(id1, id4);
assertNotEquals(null, id1);

assertEquals(id1.hashCode(), id2.hashCode());
assertNotEquals(id1.hashCode(), id3.hashCode());
}
}
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