Dynamically calculate sample identifiers in study view filter helper

cBioPortal · Dec 19, 2024 · 8607377 · 8607377
1 parent 0bc04ff
commit 8607377
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Showing 3 changed files with 11 additions and 14 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -55,7 +55,6 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil
     private final StudyViewFilter studyViewFilter;
     private final CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFilter;
     private final List<CustomSampleIdentifier> customDataSamples;
-    private final String[] filteredSampleIdentifiers;
     private final List<String> involvedCancerStudies;
 
     private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, 
@@ -66,13 +65,6 @@ private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter,
         this.categorizedGenericAssayDataCountFilter = extractGenericAssayDataCountFilters(studyViewFilter, genericAssayProfilesMap);
         this.customDataSamples = customDataSamples;
         this.involvedCancerStudies = involvedCancerStudies;
-        if (studyViewFilter != null && studyViewFilter.getSampleIdentifiers() != null) {
-            this.filteredSampleIdentifiers = studyViewFilter.getSampleIdentifiers().stream()
-                .map(sampleIdentifier -> sampleIdentifier.getStudyId() + "_" + sampleIdentifier.getSampleId())
-                .toArray(String[]::new);
-        } else {
-            this.filteredSampleIdentifiers = new String[0];
-        }
     }
 
     public StudyViewFilter studyViewFilter() {
@@ -88,7 +80,13 @@ public List<CustomSampleIdentifier> customDataSamples() {
     }
 
     public String[] filteredSampleIdentifiers() {
-        return this.filteredSampleIdentifiers;
+        if (studyViewFilter != null && studyViewFilter.getSampleIdentifiers() != null) {
+            return studyViewFilter.getSampleIdentifiers().stream()
+                .map(sampleIdentifier -> sampleIdentifier.getStudyId() + "_" + sampleIdentifier.getSampleId())
+                .toArray(String[]::new);
+        } else {
+            return new String[0];
+        }
     }
 
     public List<String> involvedCancerStudies() {

diff --git a/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java b/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java
@@ -6,7 +6,6 @@ public class CustomSampleIdentifier extends SampleIdentifier implements Serializ
 
     private boolean isFilteredOut = false;
     private String value;
-
     private String uniqueSampleId;
 
     public boolean getIsFilteredOut() {
@@ -32,6 +31,6 @@ public String getUniqueSampleId() {
         if (getStudyId() != null && getSampleId() != null) {
             return getStudyId() + "_" + getSampleId();
         }
-        return null;  // or return a default value if either studyId or sampleId is null
+        return null;  // or return null if either studyId or sampleId is null
     }
 }
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -60,14 +60,14 @@
                 )
 
             </if>
-
-            <if test="studyViewFilterHelper.filteredSampleIdentifiers != null and studyViewFilterHelper.filteredSampleIdentifiers.length > 0">
+            <bind name="filteredSampleIdentifiers" value="studyViewFilterHelper.filteredSampleIdentifiers()" />
+            <if test="filteredSampleIdentifiers != null and filteredSampleIdentifiers.length > 0">
             INTERSECT
                 SELECT sample_unique_id
                 FROM sample_derived
                 WHERE sample_unique_id IN
                 (
-                    #{studyViewFilterHelper.filteredSampleIdentifiers, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
+                    #{filteredSampleIdentifiers, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
                 )
             </if>
             <if test="studyViewFilterHelper.studyViewFilter.customDataFilters != null and !studyViewFilterHelper.studyViewFilter.customDataFilters.isEmpty() and studyViewFilterHelper.customDataSamples != null">