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Fix CNA query #11265

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merged 2 commits into from
Dec 10, 2024
Merged

Fix CNA query #11265

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a5f1a39
fix CNA query for genomic data filter
onursumer Dec 10, 2024
43c2bba
rename one of the cna_query statements to cna_count_query to avoid ta…
onursumer Dec 10, 2024
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4 changes: 2 additions & 2 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -702,7 +702,7 @@
<sql id="categoricalGenomicDataFilterForCNA">
<!-- filter on study to reduce query size in preparation of the following LEFT JOIN -->
WITH cna_query AS (
SELECT sample_unique_id, alteration_value
SELECT sample_unique_id as sampleUniqueId, alteration_value
FROM genetic_alteration_derived
WHERE profile_type = #{genomicDataFilter.profileType}
AND hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
Expand All @@ -714,7 +714,7 @@
SELECT DISTINCT sd.sample_unique_id
<!-- join with sample table to get all 'NA' samples -->
FROM sample_derived sd
LEFT JOIN cna_query ON sd.sample_unique_id = cna_query.sample_unique_id
LEFT JOIN cna_query ON sd.sample_unique_id = cna_query.sampleUniqueId
WHERE cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterHelper.studyViewFilter.studyIds" open="(" separator="," close=")">
#{studyId}
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6 changes: 3 additions & 3 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
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Expand Up @@ -258,7 +258,7 @@
<select id="getCNACounts" resultMap="GenomicDataCountItemResultMap">
<bind name="profileType" value="genomicDataFilters[0].profileType" />
<!-- get all non-NA value samples. A caveat here is that if user select only 'NA', this query will return empty (null) thus we need the 2 coalesce() below to handle this case -->
WITH cna_query as (
WITH cna_count_query as (
SELECT
hugo_gene_symbol as hugoGeneSymbol,
#{profileType} as profileType,
Expand Down Expand Up @@ -288,10 +288,10 @@
SELECT
hugoGeneSymbol,
sum(count) as cna_count
FROM cna_query
FROM cna_count_query
GROUP BY hugoGeneSymbol
)
SELECT * FROM cna_query
SELECT * FROM cna_count_query
UNION ALL
<!-- The NA count is specially caculated using total sample count minus non-NA count, therefore
these 2 coalesces are here in case the non-NA subquery returned empty results and we need to provide properties needed to construct the target object -->
Expand Down
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