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Implement custom-data-bin-counts endpoint (#10827)
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* Implement custom-data-bin-counts associated filter
* Create StudyViewFilterContext and Helper



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Co-authored-by: Bryan Lai <[email protected]>
Co-authored-by: Charles Haynes <[email protected]>
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@gblaih @haynescd
3 people authored and haynescd committed Nov 24, 2024
1 parent 6ff724d commit ff7ecbc
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Showing 31 changed files with 788 additions and 571 deletions.
11 changes: 11 additions & 0 deletions src/main/java/org/cbioportal/model/StudyViewFilterContext.java
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package org.cbioportal.model;

import org.cbioportal.web.parameter.CustomSampleIdentifier;
import org.cbioportal.web.parameter.StudyViewFilter;

import java.util.List;

public record StudyViewFilterContext( StudyViewFilter studyViewFilter,
List<CustomSampleIdentifier> customDataFilterSamples) {

}
50 changes: 25 additions & 25 deletions src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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Expand Up @@ -12,59 +12,59 @@
import org.cbioportal.model.PatientTreatment;
import org.cbioportal.model.Sample;
import org.cbioportal.model.SampleTreatment;
import org.cbioportal.model.StudyViewFilterContext;
import org.cbioportal.web.parameter.ClinicalDataType;
import org.cbioportal.web.parameter.GenomicDataFilter;
import org.cbioportal.web.parameter.StudyViewFilter;

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

public interface StudyViewRepository {
List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter);

List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterContext);
List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);

List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);

List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);

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

List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);

List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilter studyViewFilter);
List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext);

List<ClinicalAttribute> getClinicalAttributes();

Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap();

List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilter studyViewFilter);
List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);

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

int getFilteredSamplesCount(StudyViewFilter studyViewFilter);
int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext);

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

int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);
int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType);

int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, String alterationType);
int getSampleProfileCountWithoutPanelData(StudyViewFilterContext studyViewFilterContext, String alterationType);

List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilterContext studyViewFilterContext);

List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter);
List<PatientTreatment> getPatientTreatments(StudyViewFilterContext studyViewFilterContext);

int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter);
int getTotalPatientTreatmentCount(StudyViewFilterContext studyViewFilterContext);

List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter);
List<SampleTreatment> getSampleTreatments(StudyViewFilterContext studyViewFilterContext);

int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter);
int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext);

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

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

List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
}
42 changes: 36 additions & 6 deletions src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
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import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
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 class StudyViewFilterHelper {
public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter, @Nullable EnumMap<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap) {
public final class StudyViewFilterHelper {
public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter,
@Nullable Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap,
@Nullable List<CustomSampleIdentifier> customDataSamples) {
if (Objects.isNull(studyViewFilter)) {
studyViewFilter = new StudyViewFilter();
}
if (Objects.isNull(clinicalAttributesMap)) {
clinicalAttributesMap = new EnumMap<>(ClinicalAttributeDataSource.class);
}
return new StudyViewFilterHelper(studyViewFilter, clinicalAttributesMap);
if (Objects.isNull(customDataSamples)) {
customDataSamples = new ArrayList<>();
}
return new StudyViewFilterHelper(studyViewFilter, clinicalAttributesMap, customDataSamples);
}

private final StudyViewFilter studyViewFilter;
private final CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter;
private final List<CustomSampleIdentifier> customDataSamples;
private final boolean applyPatientIdFilters;


private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, @NonNull Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap ) {
private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, @NonNull Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap,
@NonNull List<CustomSampleIdentifier> customDataSamples) {
this.studyViewFilter = studyViewFilter;
this.categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter, clinicalAttributesMap);
this.customDataSamples = customDataSamples;
this.applyPatientIdFilters = shouldApplyPatientIdFilters();
}


public StudyViewFilter studyViewFilter() {
return studyViewFilter;
}

public CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter() {
return categorizedClinicalDataCountFilter;
}

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

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

if (studyViewFilter.getClinicalDataFilters() == null || clinicalAttributesMap.isEmpty()) {
Expand Down Expand Up @@ -73,6 +97,12 @@ private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final
.toList())
.build();
}


public boolean shouldApplyPatientIdFilters() {
return studyViewFilter.getClinicalEventFilters() != null && !studyViewFilter.getClinicalEventFilters().isEmpty()
|| studyViewFilter.getPatientTreatmentFilters() != null && studyViewFilter.getPatientTreatmentFilters().getFilters()!= null && !studyViewFilter.getPatientTreatmentFilters().getFilters().isEmpty()
|| categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
|| categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters().isEmpty();
}

}
52 changes: 24 additions & 28 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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package org.cbioportal.persistence.mybatisclickhouse;

import org.apache.ibatis.annotations.Param;
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.CaseListDataCount;
import org.cbioportal.model.ClinicalAttribute;
Expand All @@ -14,59 +15,54 @@
import org.cbioportal.model.Sample;
import org.cbioportal.model.SampleTreatment;
import org.cbioportal.persistence.helper.AlterationFilterHelper;
import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
import org.cbioportal.persistence.helper.StudyViewFilterHelper;
import org.cbioportal.web.parameter.GenomicDataFilter;
import org.cbioportal.web.parameter.StudyViewFilter;

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


public interface StudyViewMapper {
List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
List<Sample> getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);

List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);

List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);
List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);

List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds, List<String> filteredAttributeValues);

List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
List<CaseListDataCount> getCaseListDataCountsPerStudy(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<ClinicalAttribute> getClinicalAttributes();

List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);

List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);

List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType);

int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType);

int getTotalProfiledCountByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
int getTotalProfiledCountByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType);

int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
int getSampleProfileCountWithoutPanelData(StudyViewFilterHelper studyViewFilterHelper, String alterationType);

List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
List<ClinicalEventTypeCount> getClinicalEventTypeCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
int getPatientTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
List<SampleTreatment> getSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
int getTotalSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
List<PatientTreatment> getPatientTreatments(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
int getPatientTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
List<SampleTreatment> getSampleTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
int getTotalSampleTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);

List<GenomicDataCountItem> getCNACounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
List<GenomicDataCountItem> getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);

Map<String, Integer> getMutationCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, GenomicDataFilter genomicDataFilter);
Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);

List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
}
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