Demo rfc80 poc mutation&genomic data count unit tests

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

@@ -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

@@ -19,7 +19,6 @@
 import org.cbioportal.web.parameter.GenomicDataFilter;
 
 import java.util.List;
-import java.util.Map;
 
 
 public interface StudyViewMapper {
@@ -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

@@ -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/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));
+ List<AlterationCountByGene> alterationCountByGenes = alterationCountService.getMutatedGenes(createContext(studyViewFilter));
  for (GenomicDataFilter genomicDataFilter : genomicDataFilters) {
- Map<String, Integer> counts = studyViewRepository.getMutationCounts(createContext(studyViewFilter), genomicDataFilter);
+ AlterationCountByGene filteredAlterationCount = alterationCountByGenes.stream()
+ .filter(g -> g.getHugoGeneSymbol().equals(genomicDataFilter.getHugoGeneSymbol()))
+ .findFirst()
+ .orElse(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

@@ -270,28 +270,6 @@
  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

src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataFilterTest.java

@@ -0,0 +1,92 @@
+package org.cbioportal.persistence.mybatisclickhouse;
+
+import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.model.GenomicDataCountItem;
+import org.cbioportal.persistence.helper.StudyViewFilterHelper;
+import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
+import org.cbioportal.web.parameter.GenomicDataFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase;
+import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
+import org.springframework.context.annotation.Import;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import java.util.List;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+@RunWith(SpringRunner.class)
+@Import(MyBatisConfig.class)
+@DataJpaTest
+@DirtiesContext
+@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
+@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
+public class GenomicDataFilterTest extends AbstractTestcontainers {
+
+ private static final String STUDY_TCGA_PUB = "study_tcga_pub";
+ private static final String STUDY_ACC_TCGA = "acc_tcga";
+
+ @Autowired
+ private StudyViewMapper studyViewMapper;
+
+ @Test
+ public void getCNACounts() {
+ StudyViewFilter studyViewFilter = new StudyViewFilter();
+ studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+
+ GenomicDataFilter genomicDataFilterCNA = new GenomicDataFilter("AKT1", "cna");
+ List<GenomicDataCountItem> actualCountsCNA = studyViewMapper.getCNACounts(StudyViewFilterHelper.build(studyViewFilter, null, null), List.of(genomicDataFilterCNA));
+ List<GenomicDataCountItem> expectedCountsCNA = List.of(
+ new GenomicDataCountItem("AKT1", "cna", List.of(
+ new GenomicDataCount("Homozygously deleted", "-2", 2),
+ new GenomicDataCount("Heterozygously deleted", "-1", 2),
+ new GenomicDataCount("Diploid", "0", 2),
+ new GenomicDataCount("Gained", "1", 2),
+ new GenomicDataCount("Amplified", "2", 2),
+ new GenomicDataCount("NA", "NA", 5)
+ )));
+ assertThat(actualCountsCNA)
+ .usingRecursiveComparison()
+ .ignoringCollectionOrder()
+ .isEqualTo(expectedCountsCNA);
+
+ GenomicDataFilter genomicDataFilterGISTIC = new GenomicDataFilter("AKT1", "gistic");
+ List<GenomicDataCountItem> actualCountsGISTIC = studyViewMapper.getCNACounts(StudyViewFilterHelper.build(studyViewFilter, null, null), List.of(genomicDataFilterGISTIC));
+ List<GenomicDataCountItem> expectedCountsGISTIC = List.of(
+ new GenomicDataCountItem("AKT1", "gistic", List.of(
+ new GenomicDataCount("Homozygously deleted", "-2", 2),
+ new GenomicDataCount("Heterozygously deleted", "-1", 3),
+ new GenomicDataCount("Diploid", "0", 3),
+ new GenomicDataCount("Gained", "1", 3),
+ new GenomicDataCount("Amplified", "2", 3),
+ new GenomicDataCount("NA", "NA", 1)
+ )));
+ assertThat(actualCountsGISTIC)
+ .usingRecursiveComparison()
+ .ignoringCollectionOrder()
+ .isEqualTo(expectedCountsGISTIC);
+ }
+
+ @Test
+ public void getMutationCountsByType() {
+ StudyViewFilter studyViewFilter = new StudyViewFilter();
+ studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+
+ GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "mutation");
+ List<GenomicDataCountItem> actualMutationCountsByType = studyViewMapper.getMutationCountsByType(StudyViewFilterHelper.build(studyViewFilter, null, null), List.of(genomicDataFilterMutation));
+ List<GenomicDataCountItem> expectedMutationCountsByType = List.of(
+ new GenomicDataCountItem("AKT1", "mutations", List.of(
+ new GenomicDataCount("nonsense mutation", "nonsense_mutation", 1, 1),
+ new GenomicDataCount("missense mutation", "missense_mutation", 1, 1)
+ )));
+ assertThat(actualMutationCountsByType)
+ .usingRecursiveComparison()
+ .ignoringCollectionOrder()
+ .isEqualTo(expectedMutationCountsByType);
+ }
+}

src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java

@@ -65,7 +65,7 @@ public void getMutatedGenes() {
  AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
  assertEquals(3, alterationCountByGenes.size());
 
- var testBrca1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "brca1")).findFirst();
+ var testBrca1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "BRCA1")).findFirst();
  assert (testBrca1AlterationCount.isPresent());
  assertEquals(Integer.valueOf(5), testBrca1AlterationCount.get().getTotalCount());
  }
@@ -118,7 +118,7 @@ public void getTotalProfiledCountsByGene() {
 
  assertEquals(3, totalProfiledCountsMap.size());
 
- var akt2TotalProfiledCounts = totalProfiledCountsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("akt2")).findFirst();
+ var akt2TotalProfiledCounts = totalProfiledCountsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2")).findFirst();
  assertTrue(akt2TotalProfiledCounts.isPresent());
  assertEquals(4, akt2TotalProfiledCounts.get().getNumberOfProfiledCases().intValue());
  }