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Fix for frequency in multi-study view #11331

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Fix for frequency in multi-study view #11331

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1354c03
Fix frequency issue for same genePanel
Dec 11, 2024
0f350d2
Add sketchy fix for frequency
Dec 16, 2024
ba9b193
Start fix for general freq
Dec 19, 2024
368c13b
Start add logic for freq .1
Dec 19, 2024
c4b100f
Change lines order
Jan 13, 2025
5a157c9
Rebase with working changes
Jan 13, 2025
22078e5
Remove comment and made function
Jan 20, 2025
a533e29
Add some comments
Jan 20, 2025
94fbda8
Modify test code to test for new function/changes
Feb 3, 2025
ff17d92
Remove unused components
Feb 4, 2025
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34 changes: 34 additions & 0 deletions src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
Expand Down Expand Up @@ -280,6 +281,39 @@ private <S extends AlterationCountBase> Pair<List<S>, Long> getAlterationGeneCou
}
AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult);
});

molecularProfileCaseIdentifiers
.stream()
.collect(Collectors
.groupingBy(identifier -> molecularProfileIdStudyIdMap.get(identifier.getMolecularProfileId())))
.values()
.forEach(studyMolecularProfileCaseIdentifiers -> {
List<S> studyAlterationCountByGenes = dataFetcher.apply(studyMolecularProfileCaseIdentifiers);
if (includeFrequency) {
Long studyProfiledCasesCount = includeFrequencyFunction.apply(studyMolecularProfileCaseIdentifiers, studyAlterationCountByGenes);
profiledCasesCount.updateAndGet(v -> v + studyProfiledCasesCount);
}
Map<String, S> studyResult = new HashMap<>();
studyAlterationCountByGenes.forEach(datum -> {
String key = datum.getUniqueEventKey();
studyResult.put(key, datum);
});
List<S> allGene= new ArrayList<>(totalResult.values());
allGene.forEach(datum -> {
String key = datum.getUniqueEventKey();
S alterationCountByGene = totalResult.get(key);
alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + studyMolecularProfileCaseIdentifiers.size());
Set<String> matchingGenePanelIds = new HashSet<>();
if (!alterationCountByGene.getMatchingGenePanelIds().isEmpty()) {
matchingGenePanelIds.addAll(alterationCountByGene.getMatchingGenePanelIds());
}
if (!datum.getMatchingGenePanelIds().isEmpty()) {
matchingGenePanelIds.addAll(datum.getMatchingGenePanelIds());
}
alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
totalResult.put(key, alterationCountByGene);
});
});
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Lets break this out into functions instead of one big anonymous function. Also, can we add some comments

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@eugeniomazzone eugeniomazzone Jan 20, 2025 •
edited
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Moved the code to a separate function updateAlterationGeneCountsMap mimicking setupAlterationGeneCountsMap (see new commit at https://github.com/eugeniomazzone/cbioportal/tree/master)

alterationCountByGenes = new ArrayList<>(totalResult.values());
}
return new Pair<>(alterationCountByGenes, profiledCasesCount.get());
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java
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Expand Up @@ -148,7 +148,8 @@ public static <S extends AlterationCountBase> void setupAlterationGeneCountsMap(
S alterationCountByGene = totalResult.get(key);
alterationCountByGene.setTotalCount(alterationCountByGene.getTotalCount() + datum.getTotalCount());
alterationCountByGene.setNumberOfAlteredCases(alterationCountByGene.getNumberOfAlteredCases() + datum.getNumberOfAlteredCases());
alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + datum.getNumberOfProfiledCases());
alterationCountByGene.setNumberOfProfiledCases(0);
//alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + datum.getNumberOfProfiledCases());
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Why is it just commented out?

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@eugeniomazzone eugeniomazzone Jan 20, 2025 •
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Old line is now removed (see new commit at https://github.com/eugeniomazzone/cbioportal/tree/master)

Set<String> matchingGenePanelIds = new HashSet<>();
if (!alterationCountByGene.getMatchingGenePanelIds().isEmpty()) {
matchingGenePanelIds.addAll(alterationCountByGene.getMatchingGenePanelIds());
Expand All @@ -159,6 +160,7 @@ public static <S extends AlterationCountBase> void setupAlterationGeneCountsMap(
alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
totalResult.put(key, alterationCountByGene);
} else {
datum.setNumberOfProfiledCases(0);
totalResult.put(key, datum);
}
});
Expand Down
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