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src/test/java/org/cbioportal/infrastructure/repository/clickhouse/genomic_data/ClickhouseGenomicDataMapperTest.java

Lines changed: 22 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -119,7 +119,8 @@ public void getMutationCountsByType() {
119119
List<GenomicDataCountItem> actualMutationCountsByType =
120120
mapper.getMutationCountsByType(
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StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
122-
List.of(genomicDataFilterMutation), false);
122+
List.of(genomicDataFilterMutation),
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false);
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List<GenomicDataCountItem> expectedMutationCountsByType =
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List.of(
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new GenomicDataCountItem(
@@ -134,28 +135,29 @@ public void getMutationCountsByType() {
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.isEqualTo(expectedMutationCountsByType);
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}
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@Test
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public void getMutationCountsByTypeAddSampleId() {
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StudyViewFilter studyViewFilter = new StudyViewFilter();
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studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
141-
142-
GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "mutation");
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List<GenomicDataCountItem> mutationCountsByType =
144-
mapper.getMutationCountsByType(
145-
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
146-
List.of(genomicDataFilterMutation), true);
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148-
assertThat(mutationCountsByType)
149-
.flatExtracting(GenomicDataCountItem::getCounts)
150-
.extracting(GenomicDataCount::getSampleIds)
151-
.allSatisfy(sampleIds ->
138+
@Test
139+
public void getMutationCountsByTypeAddSampleId() {
140+
StudyViewFilter studyViewFilter = new StudyViewFilter();
141+
studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
142+
143+
GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "mutation");
144+
List<GenomicDataCountItem> mutationCountsByType =
145+
mapper.getMutationCountsByType(
146+
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
147+
List.of(genomicDataFilterMutation),
148+
true);
149+
150+
assertThat(mutationCountsByType)
151+
.flatExtracting(GenomicDataCountItem::getCounts)
152+
.extracting(GenomicDataCount::getSampleIds)
153+
.allSatisfy(
154+
sampleIds ->
152155
assertThat(sampleIds)
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.as("sampleIds should be populated when includeSampleIds=true")
154157
.isNotNull()
155-
.isNotEmpty()
156-
);
157-
}
158-
158+
.isNotEmpty());
159+
}
160+
159161
@Test
160162
public void getProteinExpressionCounts() {
161163
// Testing combined study missing samples when one lacks a relevant genomic profile

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