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Remove need to filter via Patient-IDs, All filters utilize sample-ids #10974

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Sep 5, 2024
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Remove need to filter via Patient-IDs, All filters utilize sample-ids #10974

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84 changes: 12 additions & 72 deletions src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
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Original file line number Diff line number Diff line change
@@ -1,108 +1,48 @@
package org.cbioportal.persistence.helper;

import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
import org.cbioportal.web.parameter.ClinicalDataFilter;
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 Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap,
@Nullable List<CustomSampleIdentifier> customDataSamples) {
@Nullable List<CustomSampleIdentifier> customDataSamples) {
if (Objects.isNull(studyViewFilter)) {
studyViewFilter = new StudyViewFilter();
}
if (Objects.isNull(clinicalAttributesMap)) {
clinicalAttributesMap = new EnumMap<>(ClinicalAttributeDataSource.class);
}
if (Objects.isNull(customDataSamples)) {
customDataSamples = new ArrayList<>();
}
return new StudyViewFilterHelper(studyViewFilter, clinicalAttributesMap, customDataSamples);
return new StudyViewFilterHelper(studyViewFilter, 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,
@NonNull List<CustomSampleIdentifier> customDataSamples) {
private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter,
@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()) {
return CategorizedClinicalDataCountFilter.getBuilder().build();
}

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> 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();

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();
}

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();
public boolean isCategoricalClinicalDataFilter(ClinicalDataFilter clinicalDataFilter) {
var filterValue = clinicalDataFilter.getValues().getFirst();
return filterValue.getValue() != null;
}

}
2 changes: 1 addition & 1 deletion src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterCon
}

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

@Override
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