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Genomic and Generic Assay bin counts endpoints #10964

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Sep 11, 2024
Merged

Genomic and Generic Assay bin counts endpoints #10964

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dd085ed
Genomic and Generic Assay bin counts endpoints
dippindots Aug 6, 2024
b204683
Address comments
dippindots Aug 30, 2024
002e515
add api tests in backend and skip NA mismatch tests
dippindots Sep 11, 2024
8c0f82b
Address sonorcloud issues
dippindots Sep 11, 2024
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7 changes: 7 additions & 0 deletions src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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Expand Up @@ -9,6 +9,7 @@
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.GenomicDataCountItem;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.model.PatientTreatment;
import org.cbioportal.model.Sample;
import org.cbioportal.model.SampleTreatment;
Expand Down Expand Up @@ -67,4 +68,10 @@ public interface StudyViewRepository {
Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter);

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

List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);

List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);

List<MolecularProfile> getGenericAssayProfiles();
}
4 changes: 2 additions & 2 deletions ...ce/enums/ClinicalAttributeDataSource.java → ...oportal/persistence/enums/DataSource.java
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@@ -1,11 +1,11 @@
package org.cbioportal.persistence.enums;

public enum ClinicalAttributeDataSource {
public enum DataSource {
PATIENT("PATIENT"),SAMPLE("SAMPLE");

private final String value;

ClinicalAttributeDataSource(String value) {
DataSource(String value) {
this.value = value;
}

Expand Down
75 changes: 70 additions & 5 deletions src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
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@@ -1,44 +1,109 @@
package org.cbioportal.persistence.helper;

import org.cbioportal.model.MolecularProfile;
import org.cbioportal.persistence.enums.DataSource;
import org.cbioportal.web.parameter.ClinicalDataFilter;
import org.cbioportal.web.parameter.CategorizedGenericAssayDataCountFilter;
import org.cbioportal.web.parameter.CategorizedGenomicDataCountFilter;
import org.cbioportal.web.parameter.CustomSampleIdentifier;
import org.cbioportal.web.parameter.StudyViewFilter;
import org.springframework.lang.NonNull;
import org.springframework.lang.Nullable;

import java.util.ArrayList;
import java.util.EnumMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;

public final class StudyViewFilterHelper {
public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter,
@Nullable List<CustomSampleIdentifier> customDataSamples) {
@Nullable Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap,
@Nullable List<CustomSampleIdentifier> customDataSamples) {
if (Objects.isNull(studyViewFilter)) {
studyViewFilter = new StudyViewFilter();
}
if (Objects.isNull(genericAssayProfilesMap)) {
genericAssayProfilesMap = new EnumMap<>(DataSource.class);
}
if (Objects.isNull(customDataSamples)) {
customDataSamples = new ArrayList<>();
}
return new StudyViewFilterHelper(studyViewFilter, customDataSamples);
return new StudyViewFilterHelper(studyViewFilter, genericAssayProfilesMap, customDataSamples);
}

private final StudyViewFilter studyViewFilter;
private final CategorizedGenomicDataCountFilter categorizedGenomicDataCountFilter;
private final CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFilter;
private final List<CustomSampleIdentifier> customDataSamples;

private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter,
@NonNull List<CustomSampleIdentifier> customDataSamples) {
private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter,
@NonNull Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap,
@NonNull List<CustomSampleIdentifier> customDataSamples) {
this.studyViewFilter = studyViewFilter;

this.categorizedGenomicDataCountFilter = extractGenomicDataCountFilters(studyViewFilter);
this.categorizedGenericAssayDataCountFilter = extractGenericAssayDataCountFilters(studyViewFilter, genericAssayProfilesMap);
this.customDataSamples = customDataSamples;
}

public StudyViewFilter studyViewFilter() {
return studyViewFilter;
}

public CategorizedGenomicDataCountFilter categorizedGenomicDataCountFilter() {
return categorizedGenomicDataCountFilter;
}

public CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFilter() {
return categorizedGenericAssayDataCountFilter;
}

public List<CustomSampleIdentifier> customDataSamples() {
return this.customDataSamples;
}

private CategorizedGenomicDataCountFilter extractGenomicDataCountFilters(final StudyViewFilter studyViewFilter) {
if (studyViewFilter.getGenomicDataFilters() == null)
{
return CategorizedGenomicDataCountFilter.getBuilder().build();
}

CategorizedGenomicDataCountFilter.Builder builder = CategorizedGenomicDataCountFilter.getBuilder();

builder.setSampleNumericalGenomicDataFilters(studyViewFilter.getGenomicDataFilters().stream()
.filter(genomicDataFilter -> !genomicDataFilter.getProfileType().equals("cna") && !genomicDataFilter.getProfileType().equals("gistic"))
.toList());
builder.setSampleCategoricalGenomicDataFilters(studyViewFilter.getGenomicDataFilters().stream()
.filter(genomicDataFilter -> genomicDataFilter.getProfileType().equals("cna") || genomicDataFilter.getProfileType().equals("gistic"))
.toList());
return builder.build();
}

private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilters(final StudyViewFilter studyViewFilter, Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap) {
if ((studyViewFilter.getGenericAssayDataFilters() == null || genericAssayProfilesMap.isEmpty()))
{
return CategorizedGenericAssayDataCountFilter.getBuilder().build();
}

CategorizedGenericAssayDataCountFilter.Builder builder = CategorizedGenericAssayDataCountFilter.getBuilder();

// TODO: Support patient level profiles and data filtering
List<String> sampleCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
.stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
.map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
.toList();
List<String> sampleNumericalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
.stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE"))
.map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
.toList();
builder.setSampleNumericalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
.filter(genericAssayDataFilter -> sampleNumericalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
.toList());
builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
.filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
.toList());
return builder.build();
}

public boolean isCategoricalClinicalDataFilter(ClinicalDataFilter clinicalDataFilter) {
var filterValue = clinicalDataFilter.getValues().getFirst();
Expand Down
6 changes: 6 additions & 0 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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Expand Up @@ -12,6 +12,7 @@
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.GenomicDataCountItem;
import org.cbioportal.model.PatientTreatment;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.model.Sample;
import org.cbioportal.model.SampleTreatment;
import org.cbioportal.persistence.helper.AlterationFilterHelper;
Expand Down Expand Up @@ -65,4 +66,9 @@ public interface StudyViewMapper {
Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);

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

List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);
List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);

List<MolecularProfile> getGenericAssayProfiles();
}
49 changes: 36 additions & 13 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Expand Up @@ -9,12 +9,13 @@
import org.cbioportal.model.GenomicDataCountItem;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.model.PatientTreatment;
import org.cbioportal.model.Sample;
import org.cbioportal.model.SampleTreatment;
import org.cbioportal.model.StudyViewFilterContext;
import org.cbioportal.persistence.StudyViewRepository;
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
import org.cbioportal.persistence.enums.DataSource;
import org.cbioportal.persistence.helper.AlterationFilterHelper;
import org.cbioportal.persistence.helper.StudyViewFilterHelper;
import org.cbioportal.web.parameter.ClinicalDataType;
Expand All @@ -24,6 +25,7 @@

import java.util.ArrayList;
import java.util.Collections;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
Expand All @@ -33,9 +35,9 @@
@Repository
public class StudyViewMyBatisRepository implements StudyViewRepository {

private Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap = new HashMap<>();


private Map<DataSource, List<ClinicalAttribute>> clinicalAttributesMap = new EnumMap<>(DataSource.class);
private Map<DataSource, List<MolecularProfile>> genericAssayProfilesMap = new EnumMap<>(DataSource.class);
private static final List<String> FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList();
private final StudyViewMapper mapper;

Expand Down Expand Up @@ -101,14 +103,19 @@ public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterCon
}

public StudyViewFilterHelper createStudyViewFilterHelper(StudyViewFilterContext studyViewFilterContext) {
return StudyViewFilterHelper.build(studyViewFilterContext.studyViewFilter(), studyViewFilterContext.customDataFilterSamples());
return StudyViewFilterHelper.build(studyViewFilterContext.studyViewFilter() , getGenericAssayProfilesMap(), studyViewFilterContext.customDataFilterSamples());
}

@Override
public List<ClinicalAttribute> getClinicalAttributes() {
return mapper.getClinicalAttributes();
}

@Override
public List<MolecularProfile> getGenericAssayProfiles() {
return mapper.getGenericAssayProfiles();
}

@Override
public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
if (clinicalAttributesMap.isEmpty()) {
Expand All @@ -118,11 +125,11 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
Map<String, ClinicalDataType> attributeDatatypeMap = new HashMap<>();

clinicalAttributesMap
.get(ClinicalAttributeDataSource.SAMPLE)
.get(DataSource.SAMPLE)
.forEach(attribute -> attributeDatatypeMap.put(attribute.getAttrId(), ClinicalDataType.SAMPLE));

clinicalAttributesMap
.get(ClinicalAttributeDataSource.PATIENT)
.get(DataSource.PATIENT)
.forEach(attribute -> attributeDatatypeMap.put(attribute.getAttrId(), ClinicalDataType.PATIENT));

return attributeDatatypeMap;
Expand Down Expand Up @@ -199,18 +206,34 @@ public List<SampleTreatment> getSampleTreatments(StudyViewFilterContext studyVie
public int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext) {
return mapper.getTotalSampleTreatmentCounts(createStudyViewFilterHelper(studyViewFilterContext));
}

@Override
public List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
return mapper.getGenomicDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), attributeIds);
}

@Override
public List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
return mapper.getGenericAssayDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), attributeIds);
}

private void buildClinicalAttributeNameMap() {
clinicalAttributesMap = this.getClinicalAttributes()
.stream()
.collect(Collectors.groupingBy(ca -> ca.getPatientAttribute() ? ClinicalAttributeDataSource.PATIENT : ClinicalAttributeDataSource.SAMPLE));
.collect(Collectors.groupingBy(ca -> ca.getPatientAttribute().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE));
}

private Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> getClinicalAttributeNameMap() {
if (clinicalAttributesMap.isEmpty()) {
buildClinicalAttributeNameMap();

private void buildGenericAssayProfilesMap() {
genericAssayProfilesMap = this.getGenericAssayProfiles()
.stream()
.collect(Collectors.groupingBy(ca -> ca.getPatientLevel().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE));
}

private Map<DataSource, List<MolecularProfile>> getGenericAssayProfilesMap() {
if (genericAssayProfilesMap.isEmpty()) {
buildGenericAssayProfilesMap();
}
return clinicalAttributesMap;
return genericAssayProfilesMap;
}

@Override
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/org/cbioportal/service/StudyViewColumnarService.java
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Expand Up @@ -45,6 +45,10 @@ public interface StudyViewColumnarService {
List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);

List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);

List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);

List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);

List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
}
31 changes: 21 additions & 10 deletions src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Expand Up @@ -81,6 +81,16 @@ public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewF
return treatmentCountReportService.getSampleTreatmentReport(createContext(studyViewFilter));
}

@Override
public List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
return generateDataCountItemsFromDataCounts(studyViewRepository.getGenomicDataBinCounts(createContext(studyViewFilter), filteredAttributes));
}

@Override
public List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
return generateDataCountItemsFromDataCounts(studyViewRepository.getGenericAssayDataBinCounts(createContext(studyViewFilter), filteredAttributes));
}

public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
return alterationCountService.getCnaGenes(createContext(studyViewFilter));
}
Expand All @@ -97,14 +107,7 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {

@Override
public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
return studyViewRepository.getClinicalDataCounts(createContext(studyViewFilter), filteredAttributes)
.stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId))
.entrySet().parallelStream().map(e -> {
ClinicalDataCountItem item = new ClinicalDataCountItem();
item.setAttributeId(e.getKey());
item.setCounts(e.getValue());
return item;
}).collect(Collectors.toList());
return generateDataCountItemsFromDataCounts(studyViewRepository.getClinicalDataCounts(createContext(studyViewFilter), filteredAttributes));
}

@Override
Expand Down Expand Up @@ -156,8 +159,16 @@ private StudyViewFilterContext createContext(StudyViewFilter studyViewFilter) {
List<CustomSampleIdentifier> customSampleIdentifiers = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
return new StudyViewFilterContext(studyViewFilter, customSampleIdentifiers);
}



private List<ClinicalDataCountItem> generateDataCountItemsFromDataCounts(List<ClinicalDataCount> dataCounts) {
return dataCounts.stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId))
.entrySet().parallelStream().map(e -> {
ClinicalDataCountItem item = new ClinicalDataCountItem();
item.setAttributeId(e.getKey());
item.setCounts(e.getValue());
return item;
}).toList();
}

public static List<CaseListDataCount> mergeCaseListCounts(List<CaseListDataCount> counts) {
Map<String, List<CaseListDataCount>> countsPerListType = counts.stream()
Expand Down
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