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Genomic and Generic Assay bin counts endpoints
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@dippindots
dippindots committed Aug 29, 2024
1 parent b36bffb commit dcaa432
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Showing 17 changed files with 966 additions and 82 deletions.
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();
}
108 changes: 73 additions & 35 deletions src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
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@@ -1,6 +1,7 @@
package org.cbioportal.persistence.helper;

import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
import org.cbioportal.web.parameter.CustomSampleIdentifier;
Expand All @@ -13,21 +14,26 @@
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;

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

private final StudyViewFilter studyViewFilter;
Expand All @@ -37,9 +43,10 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil


private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, @NonNull Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap,
@NonNull Map<ClinicalAttributeDataSource, List<MolecularProfile>> genericAssayProfilesMap,
@NonNull List<CustomSampleIdentifier> customDataSamples) {
this.studyViewFilter = studyViewFilter;
this.categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter, clinicalAttributesMap);
this.categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter, clinicalAttributesMap, genericAssayProfilesMap);
this.customDataSamples = customDataSamples;
this.applyPatientIdFilters = shouldApplyPatientIdFilters();
}
Expand All @@ -56,46 +63,77 @@ public List<CustomSampleIdentifier> customDataSamples() {
return this.customDataSamples;
}

private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter, Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap) {

if (studyViewFilter.getClinicalDataFilters() == null || clinicalAttributesMap.isEmpty()) {
private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter, Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap, Map<ClinicalAttributeDataSource, List<MolecularProfile>> genericAssayProfilesMap) {
if ((studyViewFilter.getClinicalDataFilters() == null || clinicalAttributesMap.isEmpty()) &&
(studyViewFilter.getGenericAssayDataFilters() == null || genericAssayProfilesMap.isEmpty()) &&
studyViewFilter.getGenomicDataFilters() == null)
{
return CategorizedClinicalDataCountFilter.getBuilder().build();
}

List<String> patientCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT)
.stream().filter(ca -> ca.getDatatype().equals("STRING"))
.map(ClinicalAttribute::getAttrId)
.toList();
CategorizedClinicalDataCountFilter.Builder builder = CategorizedClinicalDataCountFilter.getBuilder();

if (studyViewFilter.getClinicalDataFilters() != null) {
List<String> patientCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT)
.stream().filter(ca -> ca.getDatatype().equals("STRING"))
.map(ClinicalAttribute::getAttrId)
.toList();

List<String> patientNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT)
.stream().filter(ca -> ca.getDatatype().equals("NUMBER"))
.map(ClinicalAttribute::getAttrId)
.toList();
List<String> patientNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT)
.stream().filter(ca -> ca.getDatatype().equals("NUMBER"))
.map(ClinicalAttribute::getAttrId)
.toList();

List<String> sampleCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE)
.stream().filter(ca -> ca.getDatatype().equals("STRING"))
.map(ClinicalAttribute::getAttrId)
.toList();
List<String> sampleCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE)
.stream().filter(ca -> ca.getDatatype().equals("STRING"))
.map(ClinicalAttribute::getAttrId)
.toList();

List<String> sampleNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE)
.stream().filter(ca -> ca.getDatatype().equals("NUMBER"))
.map(ClinicalAttribute::getAttrId)
.toList();
List<String> sampleNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE)
.stream().filter(ca -> ca.getDatatype().equals("NUMBER"))
.map(ClinicalAttribute::getAttrId)
.toList();

builder.setPatientCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters()
.stream().filter(clinicalDataFilter -> patientCategoricalAttributes.contains(clinicalDataFilter.getAttributeId()))
.collect(Collectors.toList()))
.setPatientNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
.filter(clinicalDataFilter -> patientNumericalAttributes.contains(clinicalDataFilter.getAttributeId()))
.collect(Collectors.toList()))
.setSampleCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
.filter(clinicalDataFilter -> sampleCategoricalAttributes.contains(clinicalDataFilter.getAttributeId()))
.collect(Collectors.toList()))
.setSampleNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
.filter(clinicalDataFilter -> sampleNumericalAttributes.contains(clinicalDataFilter.getAttributeId()))
.collect(Collectors.toList()));
}
if (studyViewFilter.getGenomicDataFilters() != null) {
builder.setSampleNumericalGenomicDataFilters(studyViewFilter.getGenomicDataFilters().stream()
.filter(genomicDataFilter -> !genomicDataFilter.getProfileType().equals("cna") && !genomicDataFilter.getProfileType().equals("gistic"))
.collect(Collectors.toList()));
builder.setSampleCategoricalGenomicDataFilters(studyViewFilter.getGenomicDataFilters().stream()
.filter(genomicDataFilter -> genomicDataFilter.getProfileType().equals("cna") || genomicDataFilter.getProfileType().equals("gistic"))
.collect(Collectors.toList()));
}
if (studyViewFilter.getGenericAssayDataFilters() != null) {
// TODO: Support patient level profiles and data filtering
List<String> sampleCategoricalProfileTypes = genericAssayProfilesMap.get(ClinicalAttributeDataSource.SAMPLE)
.stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
.map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
.toList();

return CategorizedClinicalDataCountFilter.getBuilder()
.setPatientCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters()
.stream().filter(clinicalDataFilter -> patientCategoricalAttributes.contains(clinicalDataFilter.getAttributeId()))
.toList())
.setPatientNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
.filter(clinicalDataFilter -> patientNumericalAttributes.contains(clinicalDataFilter.getAttributeId()))
.toList())
.setSampleCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
.filter(clinicalDataFilter -> sampleCategoricalAttributes.contains(clinicalDataFilter.getAttributeId()))
.toList())
.setSampleNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
.filter(clinicalDataFilter -> sampleNumericalAttributes.contains(clinicalDataFilter.getAttributeId()))
.toList())
.build();
List<String> sampleNumericalProfileTypes = genericAssayProfilesMap.get(ClinicalAttributeDataSource.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()))
.collect(Collectors.toList()));
builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
.filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
.collect(Collectors.toList()));
}
return builder.build();
}

public boolean shouldApplyPatientIdFilters() {
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();
}
34 changes: 33 additions & 1 deletion src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Expand Up @@ -9,6 +9,7 @@
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;
Expand All @@ -17,8 +18,10 @@
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
import org.cbioportal.persistence.helper.AlterationFilterHelper;
import org.cbioportal.persistence.helper.StudyViewFilterHelper;
import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
import org.cbioportal.web.parameter.ClinicalDataType;
import org.cbioportal.web.parameter.GenomicDataFilter;
import org.cbioportal.web.parameter.StudyViewFilter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

Expand All @@ -34,6 +37,7 @@
public class StudyViewMyBatisRepository implements StudyViewRepository {

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


private static final List<String> FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList();
Expand Down Expand Up @@ -101,14 +105,19 @@ public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterCon
}

public StudyViewFilterHelper createStudyViewFilterHelper(StudyViewFilterContext studyViewFilterContext) {
return StudyViewFilterHelper.build(studyViewFilterContext.studyViewFilter(), getClinicalAttributeNameMap(), studyViewFilterContext.customDataFilterSamples());
return StudyViewFilterHelper.build(studyViewFilterContext.studyViewFilter(), getClinicalAttributeNameMap(), 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 Down Expand Up @@ -199,19 +208,42 @@ 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));
}

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

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

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

@Override
public List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
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);
}
24 changes: 24 additions & 0 deletions src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Expand Up @@ -81,6 +81,30 @@ public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewF
return treatmentCountReportService.getSampleTreatmentReport(createContext(studyViewFilter));
}

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

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

public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
return alterationCountService.getCnaGenes(createContext(studyViewFilter));
}
Expand Down
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