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Do not call next study view filter when no samples left #10124

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merged 2 commits into from
Apr 13, 2023
Merged

Do not call next study view filter when no samples left #10124

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61f72bf
Do not call next study view filter when no samples left
pvannierop Apr 12, 2023
f440c2c
Merge branch 'master' into pvannierop-patch-4
pvannierop Apr 13, 2023
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12 changes: 12 additions & 0 deletions web/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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) {

Expand Down Expand Up @@ -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) {

Expand Down
6 changes: 6 additions & 0 deletions web/src/main/java/org/cbioportal/web/util/appliers/AbstractPatientTreatmentFilter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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()
Expand Down
6 changes: 6 additions & 0 deletions web/src/main/java/org/cbioportal/web/util/appliers/AbstractSampleTreatmentFilter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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()
Expand Down
7 changes: 6 additions & 1 deletion web/src/main/java/org/cbioportal/web/util/appliers/ClinicalEventFilterApplier.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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());
Expand Down