Address sonorcloud issues

cBioPortal · Sep 11, 2024 · 36916d7 · 36916d7
1 parent 002e515
commit 36916d7
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Showing 4 changed files with 18 additions and 37 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -11,7 +11,7 @@
 import org.springframework.lang.Nullable;
 
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.EnumMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -24,7 +24,7 @@ public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFil
  studyViewFilter = new StudyViewFilter();
  }
  if (Objects.isNull(genericAssayProfilesMap)) {
- genericAssayProfilesMap = new HashMap<>();
+ genericAssayProfilesMap = new EnumMap<>(DataSource.class);
  }
  if (Objects.isNull(customDataSamples)) {
  customDataSamples = new ArrayList<>();

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -37,8 +37,7 @@ public class StudyViewMyBatisRepository implements StudyViewRepository {
 
  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;
 
@@ -217,25 +216,18 @@ public List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterContext st
  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() ? DataSource.PATIENT : DataSource.SAMPLE));
+ .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE));
  }
 
  private void buildGenericAssayProfilesMap() {
  genericAssayProfilesMap = this.getGenericAssayProfiles()
  .stream()
  .collect(Collectors.groupingBy(ca -> ca.getPatientLevel().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE));
  }
-
- private Map<DataSource, List<ClinicalAttribute>> getClinicalAttributeNameMap() {
- if (clinicalAttributesMap.isEmpty()) {
- buildClinicalAttributeNameMap();
- }
- return clinicalAttributesMap;
- }
 
  private Map<DataSource, List<MolecularProfile>> getGenericAssayProfilesMap() {
  if (genericAssayProfilesMap.isEmpty()) {

diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java
@@ -152,28 +152,23 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
 
  private <S extends DataBinFilter> void removeSelfFromFilter(S dataBinFilter, StudyViewFilter studyViewFilter) {
  switch (dataBinFilter) {
- case ClinicalDataBinFilter clinicalDataBinFilter -> {
- if (studyViewFilter.getClinicalDataFilters() != null) {
- studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId()));
- }
+ case ClinicalDataBinFilter clinicalDataBinFilter when studyViewFilter.getClinicalDataFilters() != null -> {
+ studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId()));
  }
- case GenomicDataBinFilter genomicDataBinFilter -> {
- if (studyViewFilter.getGenomicDataFilters() != null) {
- studyViewFilter.getGenomicDataFilters().removeIf(f ->
- f.getHugoGeneSymbol().equals(genomicDataBinFilter.getHugoGeneSymbol())
- && f.getProfileType().equals(genomicDataBinFilter.getProfileType())
- );
- }
+ case GenomicDataBinFilter genomicDataBinFilter when studyViewFilter.getGenomicDataFilters() != null -> {
+ studyViewFilter.getGenomicDataFilters().removeIf(f ->
+ f.getHugoGeneSymbol().equals(genomicDataBinFilter.getHugoGeneSymbol())
+ && f.getProfileType().equals(genomicDataBinFilter.getProfileType())
+ );
  }
- case GenericAssayDataBinFilter genericAssayDataBinFilter -> {
- if (studyViewFilter.getGenericAssayDataFilters() != null) {
- studyViewFilter.getGenericAssayDataFilters().removeIf(f ->
- f.getStableId().equals(genericAssayDataBinFilter.getStableId())
- && f.getProfileType().equals(genericAssayDataBinFilter.getProfileType())
- );
- }
+ case GenericAssayDataBinFilter genericAssayDataBinFilter when studyViewFilter.getGenericAssayDataFilters() != null -> {
+ studyViewFilter.getGenericAssayDataFilters().removeIf(f ->
+ f.getStableId().equals(genericAssayDataBinFilter.getStableId())
+ && f.getProfileType().equals(genericAssayDataBinFilter.getProfileType())
+ );
  }
  default -> {
+ // Do not remove any filters
  }
  }
  }
@@ -223,7 +218,6 @@ private <T extends DataBinFilter, U extends DataBin> List<U> calculateStaticData
 
  for (T dataBinFilter : dataBinFilters) {
  // if there is data for requested attribute
- // TODO: consider if this is correct to passing in a empty map
  if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) {
  List<U> dataBins = dataBinner
  .calculateClinicalDataBins(
@@ -252,7 +246,6 @@ private <T extends DataBinFilter, U extends DataBin> List<U> calculateDynamicDat
 
  for (T dataBinFilter : dataBinFilters) {
  // if there is data for requested attribute
- // TODO: consider if this is correct to passing in a empty map
  if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) {
  List<U> dataBins = dataBinner
  .calculateDataBins(

diff --git a/...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/...va/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java
@@ -1,8 +1,6 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 
-import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalDataCount;
-import org.cbioportal.persistence.enums.DataSource;
 import org.cbioportal.persistence.helper.StudyViewFilterHelper;
 import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
 import org.cbioportal.web.parameter.ClinicalDataFilter;
@@ -20,9 +18,7 @@
 
 import java.math.BigDecimal;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import static org.junit.Assert.assertEquals;