Adjacent merging version

cBioPortal · Dec 6, 2024 · 5892eaf · 5892eaf
1 parent 8bf6311
commit 5892eaf
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Showing 5 changed files with 78 additions and 49 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -287,7 +287,7 @@ public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewF
 
 
     private StudyViewFilterContext createContext(StudyViewFilter studyViewFilter) {
-        studyViewFilter.mergeDataFilterNumericalValues();
+        StudyViewColumnarServiceUtil.mergeDataFilterNumericalValues(studyViewFilter);
         List<CustomSampleIdentifier> customSampleIdentifiers = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
         return new StudyViewFilterContext(studyViewFilter, customSampleIdentifiers);
     }

diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java
@@ -5,14 +5,18 @@
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.web.parameter.DataFilterValue;
+import org.cbioportal.web.parameter.GenomicDataFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
 
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
-public class StudyViewColumnarServiceUtil {
+public final class StudyViewColumnarServiceUtil {
 
     private StudyViewColumnarServiceUtil() {}
 
@@ -155,5 +159,44 @@ public static List<ClinicalDataCount> normalizeDataCounts(List<ClinicalDataCount
         return new ArrayList<>(normalizedDataCounts);
     }
 
-
+    /**
+     * Merge the range of numerical bins in DataFilters to reduce the number of scans that runs on the database when filtering.
+     */
+    public static void mergeDataFilterNumericalValues(StudyViewFilter studyViewFilter) {
+        if (studyViewFilter.getGenomicDataFilters() == null || studyViewFilter.getGenomicDataFilters().isEmpty()) return;
+
+        List<GenomicDataFilter> mergedGenomicDataFilters = new ArrayList<>();
+
+        for (GenomicDataFilter genomicDataFilter : studyViewFilter.getGenomicDataFilters()) {
+            List<DataFilterValue> mergedValues = new ArrayList<>();
+
+            BigDecimal mergedStart = null, mergedEnd = null;
+            for (DataFilterValue dataFilterValue : genomicDataFilter.getValues()) {
+                // leave non-numerical values as they are
+                if (dataFilterValue.getValue() != null) {
+                    mergedValues.add(dataFilterValue);
+                }
+                // merge adjacent numerical bins
+                else {
+                    BigDecimal start = dataFilterValue.getStart();
+                    BigDecimal end = dataFilterValue.getEnd();
+
+                    if (mergedStart == null) mergedStart = start;
+                    if (mergedEnd == null) mergedEnd = end;
+                    else if (mergedEnd.equals(start)) mergedEnd = end;
+                    else {
+                        mergedValues.add(new DataFilterValue(mergedStart, mergedEnd, null));
+                        mergedStart = null;
+                        mergedEnd = null;
+                    }
+                }
+            }
+
+            mergedValues.add(new DataFilterValue(mergedStart, mergedEnd, null));
+            GenomicDataFilter mergedGenomicDataFilter = new GenomicDataFilter(genomicDataFilter.getHugoGeneSymbol(), genomicDataFilter.getProfileType(), mergedValues);
+            mergedGenomicDataFilters.add(mergedGenomicDataFilter);
+        }
+
+        studyViewFilter.setGenomicDataFilters(mergedGenomicDataFilters);
+    }
 }
diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java b/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java
@@ -1,6 +1,7 @@
 package org.cbioportal.web.parameter;
 
 import java.io.Serializable;
+import java.util.List;
 
 public class GenomicDataFilter extends DataFilter implements Serializable {
     private String hugoGeneSymbol;
@@ -13,6 +14,12 @@ public GenomicDataFilter(String hugoGeneSymbol, String profileType) {
         this.profileType = profileType;
     }
 
+    public GenomicDataFilter(String hugoGeneSymbol, String profileType, List<DataFilterValue> values) {
+        this.hugoGeneSymbol = hugoGeneSymbol;
+        this.profileType = profileType;
+        this.setValues(values);
+    }
+
     public String getHugoGeneSymbol() {
         return hugoGeneSymbol;
     }

diff --git a/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java b/src/main/java/org/cbioportal/web/parameter/StudyViewFilter.java
@@ -1,8 +1,6 @@
 package org.cbioportal.web.parameter;
 
 import java.io.Serializable;
-import java.math.BigDecimal;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 
@@ -43,7 +41,6 @@ public class StudyViewFilter implements Serializable {
     private AlterationFilter alterationFilter;
     private List<DataFilter> clinicalEventFilters;
     private List<MutationDataFilter> mutationDataFilters;
-    private static boolean areBinsMerged = false;
 
     @AssertTrue
     private boolean isEitherSampleIdentifiersOrStudyIdsPresent() {
@@ -233,46 +230,4 @@ public void setClinicalEventFilters(List<DataFilter> clinicalEventFilters) {
     public void setMutationDataFilters(List<MutationDataFilter> mutationDataFilters) {
         this.mutationDataFilters = mutationDataFilters;
     }
-
-    /**
-     * Merge the range of numerical values in DataFilters to reduce the number of scans that runs on the database.
-     * Variable 'areBinsMerged' is static so this method only gets run once.
-     */
-    public void mergeDataFilterNumericalValues() {
-        if (areBinsMerged || this.genomicDataFilters == null || this.genomicDataFilters.isEmpty()) return;
-
-        List<GenomicDataFilter> mergedGenomicDataFilters = new ArrayList<>();
-
-        for (GenomicDataFilter genomicDataFilter : this.genomicDataFilters) {
-            GenomicDataFilter mergedGenomicDataFilter = new GenomicDataFilter(genomicDataFilter.getHugoGeneSymbol(), genomicDataFilter.getProfileType());
-            List<DataFilterValue> mergedValues = new ArrayList<>();
-
-            boolean hasNullStart = false, hasNullEnd = false;
-            BigDecimal mergedStart = null, mergedEnd = null;
-            for (DataFilterValue dataFilterValue : genomicDataFilter.getValues()) {
-                // filter non-numerical values and keep them intact
-                if (dataFilterValue.getValue() != null) {
-                    mergedValues.add(dataFilterValue);
-                }
-                // record if numerical values have null start or end, otherwise record their start-end range
-                else {
-                    if (dataFilterValue.getStart() == null) hasNullStart = true;
-                    else if (mergedStart == null) mergedStart = dataFilterValue.getStart();
-                    else if (dataFilterValue.getStart().compareTo(mergedStart) < 0) mergedStart = dataFilterValue.getStart();
-                    if (dataFilterValue.getEnd() == null) hasNullEnd = true;
-                    else if (mergedEnd == null) mergedEnd = dataFilterValue.getEnd();
-                    else if (dataFilterValue.getEnd().compareTo(mergedEnd) > 0) mergedEnd = dataFilterValue.getEnd();
-                }
-            }
-            if (hasNullStart) mergedStart = null;
-            if (hasNullEnd) mergedEnd = null;
-
-            mergedValues.add(new DataFilterValue(mergedStart, mergedEnd, null));
-            mergedGenomicDataFilter.setValues(mergedValues);
-            mergedGenomicDataFilters.add(mergedGenomicDataFilter);
-        }
-
-        this.genomicDataFilters = mergedGenomicDataFilters;
-        areBinsMerged = true;
-    }
 }
diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java
@@ -5,9 +5,14 @@
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.web.parameter.DataFilterValue;
+import org.cbioportal.web.parameter.GenomicDataFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
 import org.junit.Assert;
 import org.junit.Test;
 
+import java.math.BigDecimal;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
@@ -264,5 +269,24 @@ public void testNormalizeDataCounts() {
         assertEquals(9, falseCount.getCount().intValue());
     }
 
-
+    @Test
+    public void testMergeDataFilterNumericalValues() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        List<GenomicDataFilter> genomicDataFilters = new ArrayList<>();
+        List<DataFilterValue> values = new ArrayList<>();
+        values.add(new DataFilterValue(BigDecimal.valueOf(-2.5), BigDecimal.valueOf(-2.25), null));
+        values.add(new DataFilterValue(BigDecimal.valueOf(-2.25), BigDecimal.valueOf(-2), null));
+        values.add(new DataFilterValue(BigDecimal.valueOf(-2), BigDecimal.valueOf(-1.75), null));
+        genomicDataFilters.add(new GenomicDataFilter(null, null, values));
+        studyViewFilter.setGenomicDataFilters(genomicDataFilters);
+
+        StudyViewColumnarServiceUtil.mergeDataFilterNumericalValues(studyViewFilter);
+
+        List<GenomicDataFilter> actualGenomicDataFilters = studyViewFilter.getGenomicDataFilters();
+        List<DataFilterValue> actualDataFilterValues = actualGenomicDataFilters.getFirst().getValues();
+        BigDecimal start = actualDataFilterValues.getFirst().getStart();
+        BigDecimal end = actualDataFilterValues.getFirst().getEnd();
+        assertEquals(0, BigDecimal.valueOf(-2.5).compareTo(start));
+        assertEquals(0, BigDecimal.valueOf(-1.75).compareTo(end));
+    }
 }