Do not call next study view filter when no samples left (cBioPortal#1…

…0124)
pughlab · Nov 8, 2023 · 756de51 · 756de51
1 parent 5a3479b
commit 756de51
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Showing 4 changed files with 30 additions and 1 deletion.
diff --git a/web/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/web/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java
@@ -296,6 +296,10 @@ private List<SampleIdentifier> equalityFilterClinicalData(List<SampleIdentifier>
     private List<SampleIdentifier> filterMutatedGenes(List<GeneFilter> mutatedGenefilters,
             Map<String, MolecularProfile> molecularProfileMap, List<SampleIdentifier> sampleIdentifiers) {
 
+        if (sampleIdentifiers == null || sampleIdentifiers.isEmpty()) {
+            return new ArrayList<>();
+        }
+
         for (GeneFilter genefilter : mutatedGenefilters) {
 
             List<MolecularProfile> filteredMolecularProfiles = genefilter
@@ -364,6 +368,10 @@ private List<SampleIdentifier> filterMutatedGenes(List<GeneFilter> mutatedGenefi
 
     private List<SampleIdentifier> filterStructuralVariantGenes(List<GeneFilter> svGenefilters,
             Map<String, MolecularProfile> molecularProfileMap, List<SampleIdentifier> sampleIdentifiers) {
+
+        if (sampleIdentifiers == null || sampleIdentifiers.isEmpty()) {
+            return new ArrayList<>();
+        }
 
         for (GeneFilter genefilter : svGenefilters) {
 
@@ -433,6 +441,10 @@ private List<SampleIdentifier> filterStructuralVariantGenes(List<GeneFilter> svG
 
     private List<SampleIdentifier> filterCNAGenes(List<GeneFilter> cnaGeneFilters,
             Map<String, MolecularProfile> molecularProfileMap, List<SampleIdentifier> sampleIdentifiers) {
+
+        if (sampleIdentifiers == null || sampleIdentifiers.isEmpty()) {
+            return new ArrayList<>();
+        }
 
         for (GeneFilter geneFilter : cnaGeneFilters) {
 

diff --git a/web/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java b/web/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java
@@ -8,6 +8,7 @@
 import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -25,6 +26,11 @@ public List<SampleIdentifier> filter(
         List<SampleIdentifier> identifiers,
         StudyViewFilter filter
     ) {
+
+        if (identifiers == null || identifiers.isEmpty()) {
+            return new ArrayList<>();
+        }
+
         AndedPatientTreatmentFilters filters = getFilters(filter);
 
         List<String> sampleIds = identifiers.stream()

diff --git a/web/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java b/web/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java
@@ -8,6 +8,7 @@
 import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -25,6 +26,11 @@ public List<SampleIdentifier> filter (
         List<SampleIdentifier> identifiers,
         StudyViewFilter filter
     ) {
+
+        if (identifiers == null || identifiers.isEmpty()) {
+            return new ArrayList<>();
+        }
+
         AndedSampleTreatmentFilters filters = getFilters(filter);
 
         List<String> sampleIds = identifiers.stream()

diff --git a/web/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java b/web/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java
@@ -9,6 +9,7 @@
 import org.springframework.lang.NonNull;
 import org.springframework.stereotype.Component;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
@@ -25,7 +26,11 @@ public final class ClinicalEventFilterApplier implements StudyViewSubFilterAppli
 
     @Override
     public List<SampleIdentifier> filter(@NonNull List<SampleIdentifier> toFilter, @NonNull StudyViewFilter filters) {
-
+
+       if (toFilter == null || toFilter.isEmpty()) {
+           return new ArrayList<>();
+       }
+
        List<String> studyIds = toFilter.stream()
            .map(SampleIdentifier::getStudyId)
            .collect(Collectors.toList());