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cBioPortal · Jan 3, 2025 · a3378c0 · a3378c0
1 parent baf4516
commit a3378c0
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Showing 4 changed files with 29 additions and 31 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -2,7 +2,6 @@
 
 import org.apache.ibatis.annotations.Param;
 import org.cbioportal.model.AlterationCountByGene;
-import org.cbioportal.model.AlterationEnrichment;
 import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalData;
@@ -26,7 +25,6 @@
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -91,9 +89,9 @@ public interface StudyViewMapper {
 
     List<MolecularProfile> getFilteredMolecularProfilesByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType); 
 
-    List<AlterationCountByGene> getAlterationEnrichmentCounts(List<String> sampleStableIds);
+    List<AlterationCountByGene> getAlterationEnrichmentCounts(String[] sampleStableIds);
 
-    List<SampleToPanel> getSampleToGenePanels(List<String> sampleStableIds);
+    List<SampleToPanel> getSampleToGenePanels(String[] sampleStableIds);
 
     List<GenePanelToGene> getGenePanelGenes();
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -308,7 +308,7 @@ public HashMap<String, AlterationCountByGene> getAlterationEnrichmentCounts(List
         // we need a map of panels to genes which are profiled by them
         var panelToGeneMap = getGenePanelsToGenes();
 
-        List<SampleToPanel> sampleToGenePanels = mapper.getSampleToGenePanels(sampleStableIds);
+        List<SampleToPanel> sampleToGenePanels = mapper.getSampleToGenePanels(sampleStableIds.toArray(String[]::new));
 
         // group the panels by the sample ids which they are associated with
         // this tells us for each sample, what gene panels were applied
@@ -327,7 +327,7 @@ public HashMap<String, AlterationCountByGene> getAlterationEnrichmentCounts(List
         ));
 
 
-        var alterationCounts = mapper.getAlterationEnrichmentCounts(sampleStableIds);
+        var alterationCounts = mapper.getAlterationEnrichmentCounts(sampleStableIds.toArray(String[]::new));
 
         HashMap<String, AlterationCountByGene> alteredGenesWithCounts = new HashMap();
 
@@ -379,17 +379,17 @@ public HashMap<String, AlterationCountByGene> getAlterationEnrichmentCounts(List
 
         });
 
-        alteredGenesWithCounts.entrySet().stream().forEach(n->{
-            if (geneCount.containsKey(n.getKey())) {
-                n.getValue().setNumberOfProfiledCases(
-                    geneCount.get(n.getKey()).getNumberOfProfiledCases()
-                );
-            } else {
-                n.getValue().setNumberOfProfiledCases(0);
+        geneCount.entrySet().stream().forEach(
+            n->{
+                if (alteredGenesWithCounts.containsKey(n.getKey())) {
+                    n.getValue().setNumberOfAlteredCases(
+                        alteredGenesWithCounts.get(n.getKey()).getNumberOfAlteredCases()
+                    );
+                }
             }
-        });
+        );
 
-        return alteredGenesWithCounts;
+        return geneCount;
     }
 
     public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {

diff --git a/src/main/java/org/cbioportal/web/columnar/EnrichmentsColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/EnrichmentsColumnStoreController.java
@@ -227,20 +227,18 @@ public ResponseEntity<List<AlterationEnrichment>> fetchAlterationEnrichmentsNew(
                  enrichment.setpValue(BigDecimal.valueOf(util.calculatePValue(counts)));
              }
 
+
              return enrichment;
 
          }).collect(Collectors.toList());
 
-
-
+        var filtered = alterationEnrichments.stream().filter(enrichment->{
+            // if any group has altered count above zero, let it through
+            return enrichment.getCounts().stream().anyMatch(c->c.getAlteredCount()>0);
+        }).collect(Collectors.toList());
 
-
-//        List<AlterationEnrichment> alterationEnrichments = alterationEnrichmentService.getAlterationEnrichments(
-//            groupCaseIdentifierSet,
-//            enrichmentType,
-//            alterationEventTypes);
 
-        return new ResponseEntity<>(alterationEnrichments, HttpStatus.OK);
+        return new ResponseEntity<>(filtered, HttpStatus.OK);
     }
 
 

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -6,21 +6,23 @@
     <select id="getAlterationEnrichmentCounts" resultType="org.cbioportal.model.AlterationCountByGene">
         --fudge
         SELECT hugo_gene_symbol as hugoGeneSymbol, variant_type, count(DISTINCT sample_unique_id) as numberOfAlteredCases FROM genomic_event_derived
-        WHERE sample_unique_id IN 
-        <foreach item="sampleId" collection="sampleStableIds" open="(" separator="," close=")">
-            #{sampleId}
-        </foreach>
+        WHERE sample_unique_id IN
+              (
+                  #{sampleStableIds, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
+                  )
         AND genetic_profile_stable_id IN ('genie_public_mutations','genie_public_cna','genie_public_structural_variants')
         GROUP BY (hugo_gene_symbol, variant_type)
     </select>
 
     <select id="getSampleToGenePanels" resultType="org.cbioportal.model.SampleToPanel">
-        SELECT sample_unique_id as sampleUniqueId, gene_panel_id as genePanelId, genetic_profile_id as geneticProfileId 
+        SELECT sample_unique_id as sampleUniqueId, gene_panel_id as genePanelId, genetic_profile_id as geneticProfileId
         FROM sample_to_gene_panel_derived
         WHERE sample_unique_id IN
-        <foreach item="sampleId" collection="sampleStableIds" open="(" separator="," close=")">
-            #{sampleId}
-        </foreach>
+
+        (
+          #{sampleStableIds, typeHandler=org.apache.ibatis.type.ArrayTypeHandler}
+        )
+
     </select>
 
     <select id="getGenePanelGenes" resultType="org.cbioportal.model.GenePanelToGene">