Add a second baseline group and a migration to port existing result sets

gemma-core/src/main/java/ubic/gemma/model/analysis/expression/diff/DifferentialExpressionAnalysisResultSetValueObject.java

@@ -46,6 +46,9 @@ public DifferentialExpressionAnalysisResultSetValueObject( ExpressionAnalysisRes
         if ( analysisResultSet.getBaselineGroup() != null ) {
             this.baselineGroup = new FactorValueBasicValueObject( analysisResultSet.getBaselineGroup() );
         }
+        if ( analysisResultSet.getSecondBaselineGroup() != null ) {
+            this.secondBaselineGroup = new FactorValueBasicValueObject( analysisResultSet.getSecondBaselineGroup() );
+        }
     }
 
     /**

gemma-core/src/main/java/ubic/gemma/model/analysis/expression/diff/ExpressionAnalysisResultSet.java

@@ -28,6 +28,7 @@
 import ubic.gemma.model.expression.experiment.FactorValue;
 import ubic.gemma.model.genome.Gene;
 
+import javax.annotation.Nullable;
 import javax.persistence.Transient;
 import java.util.HashSet;
 import java.util.Set;
@@ -40,7 +41,10 @@ public class ExpressionAnalysisResultSet extends FactorAssociatedAnalysisResultS
     private static final long serialVersionUID = 7226901182513177574L;
     private Integer numberOfProbesTested;
     private Integer numberOfGenesTested;
+    @Nullable
     private FactorValue baselineGroup;
+    @Nullable
+    private FactorValue secondBaselineGroup;
     private Set<DifferentialExpressionAnalysisResult> results = new HashSet<>();
     private DifferentialExpressionAnalysis analysis;
     private PvalueDistribution pvalueDistribution;
@@ -91,18 +95,38 @@ public void setAnalysis( DifferentialExpressionAnalysis analysis ) {
     }
 
     /**
-     * @return The group considered baseline when computing scores and 'upRegulated'. This might be a control group if it could
-     * be recognized. For continuous factors, this would be null. For interaction terms we do not compute this so it
-     * will also be null.
+     * The group considered baseline when computing scores and 'upRegulated'. This might be a control group if it could
+     * be recognized.
+     * <p>
+     * Corresponds to {@link ContrastResult#getFactorValue()}.
+     * <p>
+     * For interactions, {@link #getSecondBaselineGroup()} will also be populated.
+     * <p>
+     * For continuous factors, this would be {@code null}.
      */
+    @Nullable
     public FactorValue getBaselineGroup() {
         return this.baselineGroup;
     }
 
-    public void setBaselineGroup( FactorValue baselineGroup ) {
+    public void setBaselineGroup( @Nullable FactorValue baselineGroup ) {
         this.baselineGroup = baselineGroup;
     }
 
+    /**
+     * If this result set is for an interaction of factors, this is the second baseline group.
+     * <p>
+     * Corresponds to {@link ContrastResult#getSecondFactorValue()}.
+     */
+    @Nullable
+    public FactorValue getSecondBaselineGroup() {
+        return this.secondBaselineGroup;
+    }
+
+    public void setSecondBaselineGroup( @Nullable FactorValue secondBaselineGroup ) {
+        this.secondBaselineGroup = secondBaselineGroup;
+    }
+
     public Set<HitListSize> getHitListSizes() {
         return this.hitListSizes;
     }

gemma-core/src/main/java/ubic/gemma/persistence/service/analysis/expression/diff/ExpressionAnalysisResultSetDaoImpl.java

@@ -230,6 +230,15 @@ public void thaw( ExpressionAnalysisResultSet ears ) {
             Hibernate.initialize( ears.getAnalysis().getSubsetFactorValue() );
             Hibernate.initialize( ears.getAnalysis().getSubsetFactorValue().getExperimentalFactor() );
         }
+
+        if ( ears.getBaselineGroup() != null ) {
+            Hibernate.initialize( ears.getBaselineGroup() );
+            Hibernate.initialize( ears.getBaselineGroup().getExperimentalFactor() );
+        }
+        if ( ears.getSecondBaselineGroup() != null ) {
+            Hibernate.initialize( ears.getSecondBaselineGroup() );
+            Hibernate.initialize( ears.getSecondBaselineGroup().getExperimentalFactor() );
+        }
     }
 
     @Override
@@ -373,7 +382,7 @@ public Map<Long, List<Gene>> loadResultToGenesMap( ExpressionAnalysisResultSet r
      */
     private void populateBaselines( List<DifferentialExpressionAnalysisResultSetValueObject> vos ) {
         Collection<DifferentialExpressionAnalysisResultSetValueObject> vosWithMissingBaselines = vos.stream()
-                .filter( vo -> vo.getBaselineGroup() == null )
+                .filter( vo -> vo.getBaselineGroup() == null && vo.getSecondBaselineGroup() == null )
                 .collect( Collectors.toList() );
         if ( vosWithMissingBaselines.isEmpty() ) {
             return;

gemma-core/src/main/resources/sql/migrations/db.1.32.0.sql

@@ -0,0 +1,27 @@
+alter table ANALYSIS_RESULT_SET
+    add column SECOND_BASELINE_GROUP_FK BIGINT references FACTOR_VALUE (ID) after BASELINE_GROUP_FK;
+
+-- populate baselines for interaction terms
+update ANALYSIS_RESULT_SET
+    join DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT
+    on ANALYSIS_RESULT_SET.ID = DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT.RESULT_SET_FK
+    join CONTRAST_RESULT
+    on DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT.ID = CONTRAST_RESULT.DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT_FK
+
+    -- first baseline
+    join FACTOR_VALUE fv1 on CONTRAST_RESULT.FACTOR_VALUE_FK = fv1.ID
+    join ANALYSIS_RESULT_SET b1rs on b1rs.ANALYSIS_FK = ANALYSIS_RESULT_SET.ANALYSIS_FK
+    join FACTOR_VALUE b1g
+    on b1g.ID = b1rs.BASELINE_GROUP_FK and b1g.EXPERIMENTAL_FACTOR_FK = fv1.EXPERIMENTAL_FACTOR_FK
+
+    -- second baseline
+    join FACTOR_VALUE fv2 on CONTRAST_RESULT.SECOND_FACTOR_VALUE_FK = fv2.ID
+    join ANALYSIS_RESULT_SET b2rs on b2rs.ANALYSIS_FK = ANALYSIS_RESULT_SET.ANALYSIS_FK
+    join FACTOR_VALUE b2g
+    on b2g.ID = b2rs.BASELINE_GROUP_FK and b2g.EXPERIMENTAL_FACTOR_FK = fv2.EXPERIMENTAL_FACTOR_FK
+
+set ANALYSIS_RESULT_SET.BASELINE_GROUP_FK        = b1g.ID,
+    ANALYSIS_RESULT_SET.SECOND_BASELINE_GROUP_FK = b2g.ID
+
+where ANALYSIS_RESULT_SET.BASELINE_GROUP_FK is null
+  and ANALYSIS_RESULT_SET.SECOND_BASELINE_GROUP_FK is null;

gemma-core/src/main/resources/ubic/gemma/model/analysis/AnalysisResultSet.hbm.xml

@@ -38,6 +38,10 @@
                              lazy="proxy" fetch="select">
                     <column name="BASELINE_GROUP_FK" not-null="false" sql-type="BIGINT"/>
                 </many-to-one>
+                <many-to-one name="secondBaselineGroup" class="ubic.gemma.model.expression.experiment.FactorValue"
+                             lazy="proxy" fetch="select">
+                    <column name="SECOND_BASELINE_GROUP_FK" not-null="false" sql-type="BIGINT"/>
+                </many-to-one>
                 <!-- FIXME: use cascade="all" when https://github.com/PavlidisLab/Gemma/issues/825 is resolved -->
                 <set name="results" lazy="true" fetch="select" inverse="true" mutable="false">
                     <key foreign-key="DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT_RESULT_SET_FKC">