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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
2eeb7b7
Fix issues for frequency calculation
Feb 7, 2025
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22 changes: 18 additions & 4 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 @@ -11,10 +11,8 @@
import org.cbioportal.model.util.Select;
import org.cbioportal.persistence.AlterationRepository;
import org.cbioportal.persistence.MolecularProfileRepository;
import org.cbioportal.persistence.StudyViewRepository;
import org.cbioportal.service.AlterationCountService;
import org.cbioportal.service.SignificantCopyNumberRegionService;
import org.cbioportal.service.SignificantlyMutatedGeneService;

import org.cbioportal.service.util.AlterationCountServiceUtil;
import org.cbioportal.service.util.AlterationEnrichmentUtil;
import org.springframework.beans.factory.annotation.Autowired;
Expand Down Expand Up @@ -266,7 +264,8 @@ private <S extends AlterationCountBase> Pair<List<S>, Long> getAlterationGeneCou
.collect(Collectors.toMap(MolecularProfile::getStableId, MolecularProfile::getCancerStudyIdentifier));

Map<String, S> totalResult = new HashMap<>();


// Initialize mutation info for study view
molecularProfileCaseIdentifiers
.stream()
.collect(Collectors
Expand All @@ -280,6 +279,21 @@ private <S extends AlterationCountBase> Pair<List<S>, Long> getAlterationGeneCou
}
AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult);
});

// Update number of profiled case considering the whole selected sample cohort
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For this second part it looks mostly duplicated from above old code. Is this intended? Could you elaborate?

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The function's structure is mostly inspired from setupAlterationGeneCountsMap, although updateAlterationGeneCountsMap use similar arguments in a different way. In the update function, TotalResults is now used in the place of studyAlterationCountByGenes and updated with identifiers information (studyMolecularProfileCaseIdentifiers).
Additionally, I've deleted a part of the function that was duplicated and was re-updating the gene panel information.

molecularProfileCaseIdentifiers // the list of all cases in the cohort
.stream()
.collect(Collectors
.groupingBy(identifier -> molecularProfileIdStudyIdMap.get(identifier.getMolecularProfileId())))
.values()
.forEach(studyMolecularProfileCaseIdentifiers -> {
List<S> studyAlterationCountByGenes = dataFetcher.apply(studyMolecularProfileCaseIdentifiers); // the list of all genes with at least one mutation in the study
if (includeFrequency) {
Long studyProfiledCasesCount = includeFrequencyFunction.apply(studyMolecularProfileCaseIdentifiers, studyAlterationCountByGenes);
profiledCasesCount.updateAndGet(v -> v + studyProfiledCasesCount);
}
AlterationCountServiceUtil.updateAlterationGeneCountsMap(totalResult, studyMolecularProfileCaseIdentifiers); // Get study identifiers and update TotalResult
});
alterationCountByGenes = new ArrayList<>(totalResult.values());
}
return new Pair<>(alterationCountByGenes, profiledCasesCount.get());
Expand Down
18 changes: 17 additions & 1 deletion src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java
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Expand Up @@ -7,6 +7,7 @@
import org.cbioportal.model.Gistic;
import org.cbioportal.model.GisticToGene;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.model.MolecularProfileCaseIdentifier;
import org.cbioportal.model.MutSig;
import org.springframework.lang.NonNull;

Expand All @@ -15,6 +16,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.ArrayList;
import java.util.function.Function;
import java.util.stream.Collectors;

Expand Down Expand Up @@ -148,7 +150,7 @@ 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); //Set number of cases to zero
Set<String> matchingGenePanelIds = new HashSet<>();
if (!alterationCountByGene.getMatchingGenePanelIds().isEmpty()) {
matchingGenePanelIds.addAll(alterationCountByGene.getMatchingGenePanelIds());
Expand All @@ -159,10 +161,24 @@ public static <S extends AlterationCountBase> void setupAlterationGeneCountsMap(
alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
totalResult.put(key, alterationCountByGene);
} else {
datum.setNumberOfProfiledCases(0); //Ensure number of cases is initialized to zero
totalResult.put(key, datum);
}
});
}

public static <S extends AlterationCountBase> void updateAlterationGeneCountsMap(
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Also some comments explaining this function would be great. We're implementing new coding guidelines so it'll help us to add JavaDocs in the future. Thanks

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I've added some comments int he code for clarity.

Map<String, S> totalResult, // the map of all genes with at least one mutation in the whole cohort
List<MolecularProfileCaseIdentifier> studyMolecularProfileCaseIdentifiers) { // the list of all cases in the study

List<S> allGene= new ArrayList<>(totalResult.values()); // get all genes with at least one mutation in the whole cohort
allGene.forEach(datum -> { // for each gene in the whole cohort
String key = datum.getUniqueEventKey(); // get the unique key of the gene
S alterationCountByGene = totalResult.get(key); // get the gene from the map
alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + studyMolecularProfileCaseIdentifiers.size()); // the update the number of profiled cases for each study
totalResult.put(key, alterationCountByGene); // update the map
});
}


}
18 changes: 6 additions & 12 deletions src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java
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Expand Up @@ -12,8 +12,6 @@
import org.cbioportal.model.util.Select;
import org.cbioportal.persistence.AlterationRepository;
import org.cbioportal.persistence.MolecularProfileRepository;
import org.cbioportal.persistence.StudyViewRepository;
import org.cbioportal.service.SignificantlyMutatedGeneService;
import org.cbioportal.service.exception.MolecularProfileNotFoundException;
import org.cbioportal.service.util.AlterationEnrichmentUtil;
import org.cbioportal.service.util.MolecularProfileUtil;
Expand All @@ -33,11 +31,7 @@
import java.util.List;
import java.util.TreeSet;

import static org.mockito.Mockito.anyBoolean;
import static org.mockito.Mockito.anyList;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
import static org.mockito.Mockito.*;

@RunWith(MockitoJUnitRunner.class)
public class AlterationCountServiceImplTest extends BaseServiceImplTest {
Expand Down Expand Up @@ -129,7 +123,7 @@ public void getSampleAlterationGeneCounts() {
includeMissingAlterationsFromGenePanel,
alterationFilter);

verify(alterationEnrichmentUtil, times(1)).includeFrequencyForSamples(anyList(), anyList(), anyBoolean());
verify(alterationEnrichmentUtil, times(2)).includeFrequencyForSamples(anyList(), anyList(), anyBoolean());

}

Expand All @@ -149,7 +143,7 @@ public void getPatientAlterationGeneCounts() {
includeMissingAlterationsFromGenePanel,
alterationFilter);

verify(alterationEnrichmentUtil, times(1)).includeFrequencyForPatients(anyList(), anyList(), anyBoolean());
verify(alterationEnrichmentUtil, times(2)).includeFrequencyForPatients(anyList(), anyList(), anyBoolean());
}


Expand Down Expand Up @@ -208,7 +202,7 @@ public void getSampleCnaGeneCounts() {
includeMissingAlterationsFromGenePanel,
alterationFilter);

verify(alterationEnrichmentUtilCna, times(1)).includeFrequencyForSamples(anyList(), anyList(), anyBoolean());
verify(alterationEnrichmentUtilCna, times(2)).includeFrequencyForSamples(anyList(), anyList(), anyBoolean());
Assert.assertEquals(expectedCnaCountByGeneList, result.getFirst());

}
Expand All @@ -230,7 +224,7 @@ public void getPatientCnaGeneCounts() {
includeMissingAlterationsFromGenePanel,
alterationFilter);

verify(alterationEnrichmentUtilCna, times(1)).includeFrequencyForPatients(anyList(), anyList(), anyBoolean());
verify(alterationEnrichmentUtilCna, times(2)).includeFrequencyForPatients(anyList(), anyList(), anyBoolean());
Assert.assertEquals(expectedCnaCountByGeneList, result.getFirst());
}

Expand All @@ -247,7 +241,7 @@ public void getSampleStructuralVariantCounts() {
includeMissingAlterationsFromGenePanel,
alterationFilter);

verify(alterationEnrichmentUtilStructVar, times(1)).includeFrequencyForSamples(anyList(), anyList(), anyBoolean());
verify(alterationEnrichmentUtilStructVar, times(2)).includeFrequencyForSamples(anyList(), anyList(), anyBoolean());
Assert.assertEquals(expectedStructuralVariantList, result.getFirst());

}
Expand Down
67 changes: 63 additions & 4 deletions src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java
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Expand Up @@ -3,20 +3,22 @@
import org.apache.commons.math3.util.Pair;
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.AlterationCountByStructuralVariant;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.MutSig;
import org.cbioportal.model.Gistic;
import org.cbioportal.model.GisticToGene;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.model.MutSig;
import org.cbioportal.model.MolecularProfileCaseIdentifier;
import org.cbioportal.model.GisticToGene;
import org.junit.Test;

import java.math.BigDecimal;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.Arrays;
import java.util.ArrayList;

import static org.junit.Assert.*;

Expand Down Expand Up @@ -272,6 +274,24 @@ public void testSetupGisticMap() {

@Test
public void testSetupAlterationGeneCountsMapWithAlterationCountByGene() {

MolecularProfileCaseIdentifier sample1 = new MolecularProfileCaseIdentifier();
sample1.setCaseId("sample1");
sample1.setMolecularProfileId("test1");

MolecularProfileCaseIdentifier sample2 = new MolecularProfileCaseIdentifier();
sample2.setCaseId("sample2");
sample2.setMolecularProfileId("test1");

MolecularProfileCaseIdentifier sample3 = new MolecularProfileCaseIdentifier();
sample3.setCaseId("sample3");
sample3.setMolecularProfileId("test1");

List<MolecularProfileCaseIdentifier> studyMolecularProfileCaseIdentifiers = new ArrayList<MolecularProfileCaseIdentifier> ();
studyMolecularProfileCaseIdentifiers.add(sample1);
studyMolecularProfileCaseIdentifiers.add(sample2);
studyMolecularProfileCaseIdentifiers.add(sample3);

AlterationCountByGene datum1 = new AlterationCountByGene();
datum1.setHugoGeneSymbol("hugo1");
datum1.setTotalCount(1);
Expand All @@ -297,6 +317,7 @@ public void testSetupAlterationGeneCountsMapWithAlterationCountByGene() {
Map<String, AlterationCountByGene> totalResult = new HashMap<>();

AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult);
AlterationCountServiceUtil.updateAlterationGeneCountsMap(totalResult, studyMolecularProfileCaseIdentifiers);

assertEquals(2, totalResult.size());
assertTrue(totalResult.containsKey("hugo1"));
Expand All @@ -318,6 +339,24 @@ public void testSetupAlterationGeneCountsMapWithAlterationCountByGene() {

@Test
public void testSetupAlterationGeneCountsMapWithAlterationCountByStructuralVariant() {

MolecularProfileCaseIdentifier sample1 = new MolecularProfileCaseIdentifier();
sample1.setCaseId("sample1");
sample1.setMolecularProfileId("test1");

MolecularProfileCaseIdentifier sample2 = new MolecularProfileCaseIdentifier();
sample2.setCaseId("sample2");
sample2.setMolecularProfileId("test1");

MolecularProfileCaseIdentifier sample3 = new MolecularProfileCaseIdentifier();
sample3.setCaseId("sample3");
sample3.setMolecularProfileId("test1");

List<MolecularProfileCaseIdentifier> studyMolecularProfileCaseIdentifiers = new ArrayList<MolecularProfileCaseIdentifier> ();
studyMolecularProfileCaseIdentifiers.add(sample1);
studyMolecularProfileCaseIdentifiers.add(sample2);
studyMolecularProfileCaseIdentifiers.add(sample3);

AlterationCountByStructuralVariant datum1 = new AlterationCountByStructuralVariant();
datum1.setGene1HugoGeneSymbol("hugo1");
datum1.setGene2HugoGeneSymbol("hugo2");
Expand Down Expand Up @@ -346,6 +385,7 @@ public void testSetupAlterationGeneCountsMapWithAlterationCountByStructuralVaria
Map<String, AlterationCountByStructuralVariant> totalResult = new HashMap<>();

AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult);
AlterationCountServiceUtil.updateAlterationGeneCountsMap(totalResult, studyMolecularProfileCaseIdentifiers);

assertEquals(2, totalResult.size());
assertTrue(totalResult.containsKey("hugo1::hugo2"));
Expand All @@ -367,6 +407,24 @@ public void testSetupAlterationGeneCountsMapWithAlterationCountByStructuralVaria

@Test
public void testSetupAlterationGeneCountsMapWithCopyNumberCountByGene() {

MolecularProfileCaseIdentifier sample1 = new MolecularProfileCaseIdentifier();
sample1.setCaseId("sample1");
sample1.setMolecularProfileId("test1");

MolecularProfileCaseIdentifier sample2 = new MolecularProfileCaseIdentifier();
sample2.setCaseId("sample2");
sample2.setMolecularProfileId("test1");

MolecularProfileCaseIdentifier sample3 = new MolecularProfileCaseIdentifier();
sample3.setCaseId("sample3");
sample3.setMolecularProfileId("test1");

List<MolecularProfileCaseIdentifier> studyMolecularProfileCaseIdentifiers = new ArrayList<MolecularProfileCaseIdentifier> ();
studyMolecularProfileCaseIdentifiers.add(sample1);
studyMolecularProfileCaseIdentifiers.add(sample2);
studyMolecularProfileCaseIdentifiers.add(sample3);

CopyNumberCountByGene datum1 = new CopyNumberCountByGene();
datum1.setEntrezGeneId(1);
datum1.setAlteration(2);
Expand Down Expand Up @@ -395,6 +453,7 @@ public void testSetupAlterationGeneCountsMapWithCopyNumberCountByGene() {
Map<String, CopyNumberCountByGene> totalResult = new HashMap<>();

AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult);
AlterationCountServiceUtil.updateAlterationGeneCountsMap(totalResult, studyMolecularProfileCaseIdentifiers);

assertEquals(2, totalResult.size());
assertTrue(totalResult.containsKey("12"));
Expand Down