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Demo rfc80 poc mutation data count specific gene parameter #10975

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Demo rfc80 poc mutation data count specific gene parameter #10975

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7dc5c1c
Basic unit tests
fuzhaoyuan Aug 19, 2024
22da8e4
Fix on mutation counts
fuzhaoyuan Aug 28, 2024
7476bec
Add optional specific gene parameter for populateAlterationCounts
fuzhaoyuan Sep 4, 2024
72a5175
Overload methods
fuzhaoyuan Sep 5, 2024
601d340
Varargs. Need to fix filter
fuzhaoyuan Sep 6, 2024
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8 changes: 6 additions & 2 deletions src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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Expand Up @@ -29,6 +29,8 @@ public interface StudyViewRepository {

List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);

List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);
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Suggested change
List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);
Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String... genesToQuery);

This is what I want. So when calling the function you can do the following...

        studyViewRepository.getTotalProfiledCounts(studyViewFilter, alterationType, "TP53", "GENEA");
        //or
studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());

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Oh wow that's cool


List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);

Expand All @@ -43,11 +45,15 @@ public interface StudyViewRepository {
List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);

Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);

Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols);
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Change the variable name to genesToQuery


int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext);

Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType);

Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols);

int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType);

int getSampleProfileCountWithoutPanelData(StudyViewFilterContext studyViewFilterContext, String alterationType);
Expand All @@ -63,8 +69,6 @@ public interface StudyViewRepository {
int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext);

List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);

Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter);

List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
}
11 changes: 5 additions & 6 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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Expand Up @@ -19,15 +19,14 @@
import org.cbioportal.web.parameter.GenomicDataFilter;

import java.util.List;
import java.util.Map;


public interface StudyViewMapper {
List<Sample> getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, List<String> hugoGeneSymbols);
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maybe a better variable name is genesToQuery?


List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);

Expand All @@ -43,11 +42,11 @@ public interface StudyViewMapper {

List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);

List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType, List<String> hugoGeneSymbols);

int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType, List<String> hugoGeneSymbols);

int getTotalProfiledCountByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType);

Expand All @@ -62,7 +61,7 @@ public interface StudyViewMapper {

List<GenomicDataCountItem> getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);

Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);

List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);

AlterationCountByGene getMutatedGene(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String specificHugoGeneSymbol);
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Am I missing this? I don't see it defined in the xml?

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Oh sorry I must forgot to remove it

}
35 changes: 26 additions & 9 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Expand Up @@ -52,7 +52,13 @@ public List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterCon
@Override
public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),
AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()));
AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), null);
}

@Override
public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols) {
return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),
AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), hugoGeneSymbols);
}

@Override
Expand Down Expand Up @@ -142,10 +148,18 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyView
public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
return mapper.getPatientClinicalDataFromStudyViewFilter(createStudyViewFilterHelper(studyViewFilterContext), attributeIds);
}

@Override
public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType) {
return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, null)
.stream()
.collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
}

@Override
public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols) {
return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, hugoGeneSymbols)
.stream()
.collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
Expand All @@ -158,7 +172,15 @@ public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext

@Override
public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) {
return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, null)
.stream()
.collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
}

@Override
public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, List<String> hugoGeneSymbols) {
return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, hugoGeneSymbols)
.stream()
.collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
Expand Down Expand Up @@ -218,11 +240,6 @@ public List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewF

return mapper.getCNACounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters);
}

public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {

return mapper.getMutationCounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilter);
}

public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {

Expand Down
16 changes: 10 additions & 6 deletions src/main/java/org/cbioportal/service/AlterationCountService.java
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@@ -1,14 +1,16 @@
package org.cbioportal.service;

import org.apache.commons.math3.util.Pair;
import org.cbioportal.model.*;
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.AlterationCountByStructuralVariant;
import org.cbioportal.model.AlterationFilter;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.MolecularProfileCaseIdentifier;
import org.cbioportal.model.StudyViewFilterContext;
import org.cbioportal.model.util.Select;
import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
import org.cbioportal.web.parameter.CustomSampleIdentifier;
import org.cbioportal.web.parameter.SampleIdentifier;
import org.cbioportal.web.parameter.StudyViewFilter;

import java.util.List;
import java.util.Map;

public interface AlterationCountService {

Expand Down Expand Up @@ -80,8 +82,10 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
AlterationFilter alterationFilter);

List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);

Map<String, AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols);

List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);

List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);

}
23 changes: 17 additions & 6 deletions src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
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Expand Up @@ -255,26 +255,26 @@ public Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<Mole
@Override
public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
var alterationCountByGenes = studyViewRepository.getMutatedGenes(studyViewFilterContext);
return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED);
return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, null);
}

public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext) {
var copyNumberCountByGenes = studyViewRepository.getCnaGenes(studyViewFilterContext);
return populateAlterationCounts(copyNumberCountByGenes, studyViewFilterContext, AlterationType.COPY_NUMBER_ALTERATION);
return populateAlterationCounts(copyNumberCountByGenes, studyViewFilterContext, AlterationType.COPY_NUMBER_ALTERATION, null);
}

@Override
public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) {
var alterationCountByGenes = studyViewRepository.getStructuralVariantGenes(studyViewFilterContext);
return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.STRUCTURAL_VARIANT);
return populateAlterationCounts(alterationCountByGenes, studyViewFilterContext, AlterationType.STRUCTURAL_VARIANT, null);
}

private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
@NonNull StudyViewFilterContext studyViewFilterContext,
@NonNull AlterationType alterationType) {
@NonNull AlterationType alterationType, List<String> hugoGeneSymbols) {
final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString());
final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString());
var profiledCountsMap = hugoGeneSymbols == null ? studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString()) : studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), hugoGeneSymbols);
final var matchingGenePanelIdsMap = hugoGeneSymbols == null ? studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString()) : studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString(), hugoGeneSymbols);
final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());

alterationCounts.parallelStream()
Expand All @@ -294,6 +294,17 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
return alterationCounts;
}

@Override
public Map<String, AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, List<String> hugoGeneSymbols) {
List<AlterationCountByGene> alterationCounts = studyViewRepository.getMutatedGenes(studyViewFilterContext, hugoGeneSymbols);
List<AlterationCountByGene> alterationCountByGenes = populateAlterationCounts(alterationCounts, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, hugoGeneSymbols);
return alterationCountByGenes.stream()
.collect(Collectors.toMap(
AlterationCountByGene::getHugoGeneSymbol,
alterationCountByGene -> alterationCountByGene,
(existing, replacement) -> existing
));
}

private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING)
Expand Down
18 changes: 11 additions & 7 deletions src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Expand Up @@ -133,15 +133,19 @@ public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter stu
@Override
public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();
int totalCount = studyViewRepository.getFilteredSamplesCount(createContext(studyViewFilter));
List<String> hugoGeneSymbols = genomicDataFilters.stream()
.map(GenomicDataFilter::getHugoGeneSymbol)
.toList();
Map<String, AlterationCountByGene> alterationCountByGenes = alterationCountService.getMutatedGenes(createContext(studyViewFilter), hugoGeneSymbols);
for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
Map<String, Integer> counts = studyViewRepository.getMutationCounts(createContext(studyViewFilter), genomicDataFilter);
AlterationCountByGene filteredAlterationCount = alterationCountByGenes.getOrDefault(genomicDataFilter.getHugoGeneSymbol(), new AlterationCountByGene());
int mutatedCount = filteredAlterationCount.getNumberOfAlteredCases();
int profiledCount = filteredAlterationCount.getNumberOfProfiledCases();
List<GenomicDataCount> genomicDataCountList = new ArrayList<>();
if (counts.getOrDefault("mutatedCount", 0) > 0)
genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get("mutatedCount"), counts.get("mutatedCount")));
if (counts.getOrDefault("notMutatedCount", 0) > 0)
genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", counts.get("notMutatedCount"), counts.get("notMutatedCount")));
if (counts.getOrDefault("notProfiledCount", 0) > 0)
genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", counts.get("notProfiledCount"), counts.get("notProfiledCount")));
genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", mutatedCount, mutatedCount));
genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", profiledCount - mutatedCount, profiledCount - mutatedCount));
genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", totalCount - profiledCount, totalCount - profiledCount));
genomicDataCountItemList.add(new GenomicDataCountItem(genomicDataFilter.getHugoGeneSymbol(), "mutations", genomicDataCountList));
}
return genomicDataCountItemList;
Expand Down
7 changes: 7 additions & 0 deletions src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java
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Expand Up @@ -6,6 +6,13 @@ public class GenomicDataFilter extends DataFilter implements Serializable {
private String hugoGeneSymbol;
private String profileType;

public GenomicDataFilter() {}

public GenomicDataFilter(String hugoGeneSymbol, String profileType) {
this.hugoGeneSymbol = hugoGeneSymbol;
this.profileType = profileType;
}

public String getHugoGeneSymbol() {
return hugoGeneSymbol;
}
Expand Down
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