Remove need to filter via Patient-IDs, All filters utilize sample-ids (…

…#10974)

src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java

@@ -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;
  }
 
 }

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java

@@ -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