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Fix GeneFilters
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@haynescd
haynescd committed Jul 18, 2023
1 parent e0e441d commit ccdb8eb
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Showing 2 changed files with 74 additions and 36 deletions.
24 changes: 11 additions & 13 deletions ...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -160,26 +160,24 @@
</foreach>
</if>
<if test="studyViewFilter.geneFilters != null and !studyViewFilter.geneFilters.isEmpty()">
INTERSECT
SELECT sample_unique_id
FROM genomic_event
<where>
<trim prefixOverrides="OR">
<foreach item="profileGroup" collection="studyViewFilter.geneFilters" open="OR (" separator="," close=")">
<foreach item="profileGroup" collection="studyViewFilter.geneFilters">
<foreach item="geneFilterQueryList" collection="profileGroup.getGeneQueries()" open="INTERSECT" separator="INTERSECT">
SELECT sample_unique_id
FROM genomic_event
<where>
genetic_profile_stable_id IN
<foreach item="molecularProfileId" collection="profileGroup.getMolecularProfileIds()" open="(" separator="," close=")">
#{molecularProfileId}
</foreach>
AND hugo_gene_symbol IN (
<foreach item="geneFilterQueryList" collection="profileGroup.getGeneQueries()" separator=",">
<foreach item="geneFilterQuery" collection="geneFilterQueryList" separator=",">
#{geneFilterQuery.hugoGeneSymbol}
</foreach>
<foreach item="geneFilterQuery" collection="geneFilterQueryList" separator=",">
#{geneFilterQuery.hugoGeneSymbol}
</foreach>
)
</foreach>
</trim>
</where>
</where>

</foreach>
</foreach>
</if>
<if test="categorizedClinicalDataCountFilter.getSampleNumericalClinicalDataFilters() != null and !categorizedClinicalDataCountFilter.getSampleNumericalClinicalDataFilters().isEmpty()">
<foreach item="clinicalDataFilter" collection="categorizedClinicalDataCountFilter.getSampleNumericalClinicalDataFilters()" open="INTERSECT" separator="INTERSECT">
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86 changes: 63 additions & 23 deletions ...st/java/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMyBatisRepositoryTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.Gene;
import org.cbioportal.model.Sample;
import org.cbioportal.model.util.Select;
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
Expand Down Expand Up @@ -102,7 +103,7 @@ public void getMutatedGenesFiltered() {
StudyViewGeneFilter mutationStudyViewGeneFilter = new StudyViewGeneFilter();
mutationStudyViewGeneFilter.setMolecularProfileIds(new HashSet<>(Arrays.asList("msk_impact_2017_mutations")));

mutationStudyViewGeneFilter.setGeneQueries(getFilters.apply("moo"));
mutationStudyViewGeneFilter.setGeneQueries(generateGeneFilters(List.of("SMARCD1", "TP53"), false));

studyViewGeneFilters.add(mutationStudyViewGeneFilter);

Expand Down Expand Up @@ -147,8 +148,8 @@ private ClinicalDataFilter generateClinicalDataFilter(String attributeId, String
return dataFilterValue;
};

private final Function<String,List<List<GeneFilterQuery>>> getFilters = v -> {

private List<List<GeneFilterQuery>> generateGeneFilters(List<String> genesToFilter, boolean createOrRelationship) {
boolean includeDriver = true;
boolean includeVUS = true;
boolean includeUnknownOncogenicity = true;
Expand All @@ -157,27 +158,25 @@ private ClinicalDataFilter generateClinicalDataFilter(String attributeId, String
boolean includeUnknownStatus = true;
Select<String> selectedTiers = Select.none();
boolean includeUnknownTier = true;

GeneFilterQuery geneFilterQuery1 = new GeneFilterQuery("SMARCD1", null,
null, includeDriver, includeVUS, includeUnknownOncogenicity, selectedTiers, includeUnknownTier,
includeGermline, includeSomatic, includeUnknownStatus);

GeneFilterQuery geneFilterQuery2 = new GeneFilterQuery("TP53", null,
null, includeDriver, includeVUS, includeUnknownOncogenicity, selectedTiers, includeUnknownTier,
includeGermline, includeSomatic, includeUnknownStatus);

List<List<GeneFilterQuery>> q1 = new ArrayList<>();
List<GeneFilterQuery> q2 = new ArrayList<>();
List<GeneFilterQuery> q3 = new ArrayList<>();

q2.add(geneFilterQuery1);
q3.add(geneFilterQuery2);
q1.add(q2);
q1.add(q3);
return q1;

};

if(createOrRelationship) {
List<GeneFilterQuery> ordGeneFilters = genesToFilter.stream().map(geneToFilter -> new GeneFilterQuery(geneToFilter,
null, null, includeDriver, includeVUS, includeUnknownOncogenicity, selectedTiers,
includeUnknownTier, includeGermline, includeSomatic, includeUnknownStatus))
.collect(Collectors.toList());

return List.of(ordGeneFilters);
} else {
List<List<GeneFilterQuery>> filter = new ArrayList<>();
for (String geneToFilter : genesToFilter) {

filter.add(List.of( new GeneFilterQuery(geneToFilter, null,
null, includeDriver, includeVUS, includeUnknownOncogenicity, selectedTiers, includeUnknownTier,
includeGermline, includeSomatic, includeUnknownStatus)));
}
return filter;
}
}

private final Function<String, DataFilterValue> mapNumericalValues = v -> {
DataFilterValue dataFilterValue = new DataFilterValue();
Expand Down Expand Up @@ -312,4 +311,45 @@ public void getClinicalDataCounts() {

Assert.assertEquals(counts.size(), 2);
}

@Test
public void getFilteredSamplesWithGeneFilters() {
StudyViewFilter studyViewFilter = generateStudyViewFilter(new String[]{"msk_impact_2017"}, null);

List<StudyViewGeneFilter> studyViewGeneFilters = new ArrayList<>();
StudyViewGeneFilter mutationStudyViewGeneFilter = new StudyViewGeneFilter();
mutationStudyViewGeneFilter.setMolecularProfileIds(new HashSet<>(List.of("msk_impact_2017_mutations")));
mutationStudyViewGeneFilter.setGeneQueries(generateGeneFilters(List.of("KRAS", "TP53"), false));
studyViewGeneFilters.add(mutationStudyViewGeneFilter);

studyViewFilter.setGeneFilters(studyViewGeneFilters);

List<Sample> samples = studyViewMyBatisRepository.getFilteredSamplesFromColumnstore(studyViewFilter, CategorizedClinicalDataCountFilter.getBuilder().build());
Assert.assertEquals(845, samples.size());

mutationStudyViewGeneFilter.setGeneQueries(generateGeneFilters(List.of("SMARCD1", "TP53"), true));
List<Sample> samplesFilteredViaOrRelationship = studyViewMyBatisRepository.getFilteredSamplesFromColumnstore(studyViewFilter, CategorizedClinicalDataCountFilter.getBuilder().build());
Assert.assertEquals(4561, samplesFilteredViaOrRelationship.size());
}

@Test
public void getFilteredSamplesWithMultipleStudyViewGeneFilters() {
StudyViewFilter studyViewFilter = generateStudyViewFilter(new String[]{"msk_impact_2017"}, null);

List<StudyViewGeneFilter> studyViewGeneFilters = new ArrayList<>();
StudyViewGeneFilter mutationStudyViewGeneFilter = new StudyViewGeneFilter();
mutationStudyViewGeneFilter.setMolecularProfileIds(new HashSet<>(List.of("msk_impact_2017_mutations")));
mutationStudyViewGeneFilter.setGeneQueries(generateGeneFilters(List.of("TP53"), false));

StudyViewGeneFilter cnaStudyViewGeneFilter = new StudyViewGeneFilter();
cnaStudyViewGeneFilter.setMolecularProfileIds(new HashSet<>(List.of("msk_impact_2017_structural_variants")));
cnaStudyViewGeneFilter.setGeneQueries(generateGeneFilters(List.of("BRAF"), true));
studyViewGeneFilters.add(mutationStudyViewGeneFilter);
studyViewGeneFilters.add(cnaStudyViewGeneFilter);

studyViewFilter.setGeneFilters(studyViewGeneFilters);

List<Sample> samples = studyViewMyBatisRepository.getFilteredSamplesFromColumnstore(studyViewFilter, CategorizedClinicalDataCountFilter.getBuilder().build());
Assert.assertEquals(16, samples.size());
}
}

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