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add custom driver filtering unit tests
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Bryan Lai committed Nov 7, 2024
1 parent 5ccee88 commit 062972f
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6 changes: 5 additions & 1 deletion src/main/resources/db-scripts/clickhouse/clickhouse.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -110,13 +110,17 @@ SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) AS sample_uniqu
me.protein_change AS mutation_variant,
me.mutation_type AS mutation_type,
mutation.mutation_status AS mutation_status,
'NA' AS driver_filter,
ada.driver_filter AS driver_filter,
'NA' AS drivet_tiers_filter,
NULL AS cna_alteration,
'' AS cna_cytoband,
'' AS sv_event_info,
concat(cs.cancer_study_identifier, '_', patient.stable_id) AS patient_unique_id
FROM mutation
INNER JOIN alteration_driver_annotation ada
ON mutation.mutation_event_id = ada.alteration_event_id
AND mutation.sample_id = ada.sample_id
AND mutation.genetic_profile_id = ada.genetic_profile_id
INNER JOIN mutation_event AS me ON mutation.mutation_event_id = me.mutation_event_id
INNER JOIN sample_profile sp
ON mutation.sample_id = sp.sample_id AND mutation.genetic_profile_id = sp.genetic_profile_id
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98 changes: 98 additions & 0 deletions src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,104 @@ public void getMutatedGenesWithAlterationFilter() {
var alterationCountByGenes2 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyMutationStatusFilter));
assertEquals(1, alterationCountByGenes2.size());

// Testing custom driver filter
AlterationFilter onlyDriverFilter = new AlterationFilter();
onlyDriverFilter.setIncludeDriver(true);
onlyDriverFilter.setIncludeVUS(false);
onlyDriverFilter.setIncludeUnknownOncogenicity(false);

var alterationCountByGenes3 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyDriverFilter));
assertEquals(2, alterationCountByGenes3.size());

var akt1AlteredCounts3 = alterationCountByGenes3.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT1"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(1, akt1AlteredCounts3);
var akt2AlteredCounts3 = alterationCountByGenes3.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(0, akt2AlteredCounts3);
var brca1AlteredCounts3 = alterationCountByGenes3.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA1"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(3, brca1AlteredCounts3);

AlterationFilter onlyVUSFilter = new AlterationFilter();
onlyVUSFilter.setIncludeDriver(false);
onlyVUSFilter.setIncludeVUS(true);
onlyVUSFilter.setIncludeUnknownOncogenicity(false);

var alterationCountByGenes4 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyVUSFilter));
assertEquals(3, alterationCountByGenes4.size());

var akt1AlteredCounts4 = alterationCountByGenes4.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT1"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(1, akt1AlteredCounts4);
var akt2AlteredCounts4 = alterationCountByGenes4.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(1, akt2AlteredCounts4);
var brca1AlteredCounts4 = alterationCountByGenes4.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA1"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(2, brca1AlteredCounts4);

AlterationFilter onlyUnknownOncogenicityFilter = new AlterationFilter();
onlyUnknownOncogenicityFilter.setIncludeDriver(false);
onlyUnknownOncogenicityFilter.setIncludeVUS(false);
onlyUnknownOncogenicityFilter.setIncludeUnknownOncogenicity(true);

var alterationCountByGenes5 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyUnknownOncogenicityFilter));
assertEquals(0, alterationCountByGenes5.size());
}

@Test
public void getCnaGenesWithAlterationFilter() {
StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));

// Create AlterationFilter
// Testing custom driver filter
AlterationFilter onlyDriverFilter = new AlterationFilter();
onlyDriverFilter.setIncludeDriver(true);
onlyDriverFilter.setIncludeVUS(false);
onlyDriverFilter.setIncludeUnknownOncogenicity(false);

var alterationCountByGenes = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyDriverFilter));
assertEquals(0, alterationCountByGenes.size());

AlterationFilter onlyVUSFilter = new AlterationFilter();
onlyVUSFilter.setIncludeDriver(false);
onlyVUSFilter.setIncludeVUS(true);
onlyVUSFilter.setIncludeUnknownOncogenicity(false);

var alterationCountByGenes1 = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyVUSFilter));
assertEquals(0, alterationCountByGenes1.size());

AlterationFilter onlyUnknownOncogenicityFilter = new AlterationFilter();
onlyUnknownOncogenicityFilter.setIncludeDriver(false);
onlyUnknownOncogenicityFilter.setIncludeVUS(false);
onlyUnknownOncogenicityFilter.setIncludeUnknownOncogenicity(true);

var alterationCountByGenes2 = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
AlterationFilterHelper.build(onlyUnknownOncogenicityFilter));
assertEquals(3, alterationCountByGenes2.size());

var akt1AlteredCounts2 = alterationCountByGenes2.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT1"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(2, akt1AlteredCounts2);
var akt2AlteredCounts2 = alterationCountByGenes2.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2"))
.mapToInt(c -> c.getNumberOfAlteredCases().intValue())
.sum();
assertEquals(1, akt2AlteredCounts2);
}

@Test
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