Genomic and Generic Assay bin counts endpoints

src/main/java/org/cbioportal/persistence/StudyViewRepository.java

@@ -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;
@@ -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();
 }

src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataSource.java → src/main/java/org/cbioportal/persistence/enums/DataSource.java

@@ -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;
  }
 

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

@@ -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();

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

@@ -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;
@@ -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();
 }

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

@@ -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;
@@ -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;
@@ -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;
 
@@ -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()) {
@@ -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;
@@ -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

src/main/java/org/cbioportal/service/StudyViewColumnarService.java

@@ -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);
 }

src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java

@@ -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));
  }
@@ -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
@@ -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()