Demo rfc80 poc mutation data count specific gene parameter

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

@@ -27,7 +27,7 @@ public interface StudyViewRepository {
 
  List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);
 
- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String... hugoGeneSymbols);
 
  List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
  List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);
@@ -42,11 +42,11 @@ public interface StudyViewRepository {
 
  List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext);
 
- Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType);
+ Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String... hugoGeneSymbols);
 
  int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext);
 
- Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType);
+ Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, String... hugoGeneSymbols);
 
  int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType);
 
@@ -63,8 +63,6 @@ public interface StudyViewRepository {
  int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext);
 
  List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
-
- Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter);
 
  List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
 }

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

@@ -19,15 +19,14 @@
 import org.cbioportal.web.parameter.GenomicDataFilter;
 
 import java.util.List;
-import java.util.Map;
 
 
 public interface StudyViewMapper {
  List<Sample> getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
  List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
- List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
+ List<AlterationCountByGene> getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper, String... hugoGeneSymbols);
 
  List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
 
@@ -43,11 +42,11 @@ public interface StudyViewMapper {
 
  List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds);
 
- List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
+ List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType, String... hugoGeneSymbols);
 
  int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
- List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
+ List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType, String... hugoGeneSymbols);
 
  int getTotalProfiledCountByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType);
 
@@ -62,7 +61,5 @@ public interface StudyViewMapper {
 
  List<GenomicDataCountItem> getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
 
- Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);
-
  List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
 }

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

@@ -48,11 +48,11 @@ public StudyViewMyBatisRepository(StudyViewMapper mapper) {
  public List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterContext) {
  return mapper.getFilteredSamples(createStudyViewFilterHelper(studyViewFilterContext));
  }
- 
+
  @Override
- public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
+ public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String... hugoGeneSymbols) {
  return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),
- AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()));
+ AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter()), hugoGeneSymbols);
  }
 
  @Override
@@ -144,8 +144,8 @@ public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyVie
  }
 
  @Override
- public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType) {
- return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
+ public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, String... hugoGeneSymbols) {
+ return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, hugoGeneSymbols)
  .stream()
  .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
  Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
@@ -157,8 +157,8 @@ public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext
  }
 
  @Override
- public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) {
- return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType)
+ public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType, String... hugoGeneSymbols) {
+ return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType, hugoGeneSymbols)
  .stream()
  .collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
  Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
@@ -218,11 +218,6 @@ public List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewF
 
  return mapper.getCNACounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters);
  }
-
- public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {
-
- return mapper.getMutationCounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilter);
- }
 
  public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
 

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

@@ -1,14 +1,16 @@
 package org.cbioportal.service;
 
 import org.apache.commons.math3.util.Pair;
-import org.cbioportal.model.*;
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.AlterationCountByStructuralVariant;
+import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.MolecularProfileCaseIdentifier;
+import org.cbioportal.model.StudyViewFilterContext;
 import org.cbioportal.model.util.Select;
-import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
-import org.cbioportal.web.parameter.CustomSampleIdentifier;
-import org.cbioportal.web.parameter.SampleIdentifier;
-import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
+import java.util.Map;
 
 public interface AlterationCountService {
 
@@ -80,8 +82,10 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
  AlterationFilter alterationFilter);
 
  List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext);
+
+ Map<String, AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String[] hugoGeneSymbols); 
+
  List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);
 
  List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
-
 }

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

@@ -271,10 +271,10 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterCont
 
  private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
  @NonNull StudyViewFilterContext studyViewFilterContext,
- @NonNull AlterationType alterationType) {
+ @NonNull AlterationType alterationType, String... hugoGeneSymbols) {
  final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
- var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString());
- final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString());
+ var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), hugoGeneSymbols);
+ final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString(), hugoGeneSymbols);
  final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());
 
  alterationCounts.parallelStream()
@@ -294,6 +294,17 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
  return alterationCounts;
  }
 
+ @Override
+ public Map<String, AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext, String[] hugoGeneSymbols) {
+ List<AlterationCountByGene> alterationCounts = studyViewRepository.getMutatedGenes(studyViewFilterContext, hugoGeneSymbols);
+ List<AlterationCountByGene> alterationCountByGenes = populateAlterationCounts(alterationCounts, studyViewFilterContext, AlterationType.MUTATION_EXTENDED, hugoGeneSymbols);
+ return alterationCountByGenes.stream()
+ .collect(Collectors.toMap(
+ AlterationCountByGene::getHugoGeneSymbol,
+ alterationCountByGene -> alterationCountByGene,
+ (existing, replacement) -> existing
+ ));
+ }
 
  private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
  return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) 

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

@@ -133,15 +133,19 @@ public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter stu
  @Override
  public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
  List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();
+ int totalCount = studyViewRepository.getFilteredSamplesCount(createContext(studyViewFilter));
+ String[] hugoGeneSymbols = genomicDataFilters.stream()
+ .map(GenomicDataFilter::getHugoGeneSymbol)
+ .toArray(String[]::new);
+ Map<String, AlterationCountByGene> alterationCountByGenes = alterationCountService.getMutatedGenes(createContext(studyViewFilter), hugoGeneSymbols);
  for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
- Map<String, Integer> counts = studyViewRepository.getMutationCounts(createContext(studyViewFilter), genomicDataFilter);
+ AlterationCountByGene filteredAlterationCount = alterationCountByGenes.getOrDefault(genomicDataFilter.getHugoGeneSymbol(), new AlterationCountByGene());
+ int mutatedCount = filteredAlterationCount.getNumberOfAlteredCases();
+ int profiledCount = filteredAlterationCount.getNumberOfProfiledCases();
  List<GenomicDataCount> genomicDataCountList = new ArrayList<>();
- if (counts.getOrDefault("mutatedCount", 0) > 0)
- genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get("mutatedCount"), counts.get("mutatedCount")));
- if (counts.getOrDefault("notMutatedCount", 0) > 0)
- genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", counts.get("notMutatedCount"), counts.get("notMutatedCount")));
- if (counts.getOrDefault("notProfiledCount", 0) > 0)
- genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", counts.get("notProfiledCount"), counts.get("notProfiledCount")));
+ genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", mutatedCount, mutatedCount));
+ genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", profiledCount - mutatedCount, profiledCount - mutatedCount));
+ genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", totalCount - profiledCount, totalCount - profiledCount));
  genomicDataCountItemList.add(new GenomicDataCountItem(genomicDataFilter.getHugoGeneSymbol(), "mutations", genomicDataCountList));
  }
  return genomicDataCountItemList;

src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java

@@ -6,6 +6,13 @@ public class GenomicDataFilter extends DataFilter implements Serializable {
  private String hugoGeneSymbol;
  private String profileType;
 
+ public GenomicDataFilter() {}
+
+ public GenomicDataFilter(String hugoGeneSymbol, String profileType) {
+ this.hugoGeneSymbol = hugoGeneSymbol;
+ this.profileType = profileType;
+ }
+
  public String getHugoGeneSymbol() {
  return hugoGeneSymbol;
  }

src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml

@@ -30,6 +30,13 @@
  FROM genomic_event_derived
  <where>
  variant_type = 'mutation' AND
+ <if test="hugoGeneSymbols != null and hugoGeneSymbols.length > 0">
+ hugo_gene_symbol IN
+ <foreach item="hugoGeneSymbol" collection="hugoGeneSymbols" open="(" separator="," close=")">
+ #{hugoGeneSymbol}
+ </foreach>
+ AND
+ </if>
  <include refid="applyStudyViewFilter">
  <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
  </include>
@@ -268,28 +275,6 @@
  FROM cna_sum
  </select>
 
- <!-- for /mutation-data-counts/fetch (returns GenomicDataCountItem objects) mutation counts pie chart part -->
- <select id="getMutationCounts">
- WITH profiled_count as (
- SELECT count(distinct sgp.sample_unique_id)
- FROM sample_to_gene_panel_derived sgp
- JOIN gene_panel_to_gene_derived gpg ON sgp.gene_panel_id = gpg.gene_panel_id
- WHERE sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
- AND gpg.gene = #{genomicDataFilter.hugoGeneSymbol}
- ),
- mutated_count as (
- SELECT count(distinct sample_unique_id)
- FROM genomic_event_derived
- WHERE sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
- AND hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
- AND variant_type = 'mutation'
- )
- SELECT
- cast((SELECT * FROM mutated_count) as INTEGER) as mutatedCount,
- cast(((SELECT * FROM profiled_count) - (SELECT * FROM mutated_count)) as INTEGER) as notMutatedCount,
- cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - (SELECT * FROM profiled_count)) as INTEGER) as notProfiledCount
- </select>
-
  <!-- for /mutation-data-counts/fetch - (returns GenomicDataCountItem objects) mutation type counts table part-->
  <select id="getMutationCountsByType" resultMap="GenomicDataCountItemResultMap">
  SELECT
@@ -356,6 +341,12 @@
  INNER JOIN gene_panel_to_gene_derived gptg on stgp.gene_panel_id = gptg.gene_panel_id
  <where>
  stgp.alteration_type = '${alterationType}'
+ <if test="hugoGeneSymbols != null and hugoGeneSymbols.length > 0">
+ AND gptg.gene IN
+ <foreach item="hugoGeneSymbol" collection="hugoGeneSymbols" open="(" separator="," close=")">
+ #{hugoGeneSymbol}
+ </foreach>
+ </if>
  AND stgp.gene_panel_id != 'WES'
  AND
  <include refid="applyStudyViewFilter">
@@ -415,6 +406,12 @@
  </include>
  </where>
  )
+ <if test="hugoGeneSymbols != null and hugoGeneSymbols.length > 0">
+ AND gene IN
+ <foreach item="hugoGeneSymbol" collection="hugoGeneSymbols" open="(" separator="," close=")">
+ #{hugoGeneSymbol}
+ </foreach>
+ </if>
  </where>
  GROUP BY gene, gene_panel_id;
  </select>