Fix when subqueries return empty for NA counts

src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml

@@ -247,8 +247,10 @@
  FROM genetic_alteration_derived
  <where>
  alteration_value != 'NA' AND
- profile_type = #{profileType}
- AND sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
+ profile_type = #{profileType} AND
+ <include refid="applyStudyViewFilter">
+ <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+ </include>
  <foreach item="genomicDataFilter" collection="genomicDataFilters" open=" AND (" separator=" OR " close=")">
  hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
  </foreach>
@@ -267,12 +269,11 @@
  SELECT * FROM cna_query
  UNION ALL
  SELECT
- hugoGeneSymbol,
+ coalesce((SELECT hugoGeneSymbol FROM cna_sum LIMIT 1), #{genomicDataFilters[0].hugoGeneSymbol}) as hugoGeneSymbol,
  #{profileType},
  'NA' as label,
  'NA' as value,
- cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - cna_count) as INTEGER) as count
- FROM cna_sum
+ cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - coalesce((SELECT cna_count FROM cna_sum LIMIT 1), 0)) as INTEGER) as count
  </select>
 
  <!-- for /mutation-data-counts/fetch (returns GenomicDataCountItem objects) mutation counts pie chart part -->
@@ -281,14 +282,20 @@
  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"/>)
+ WHERE
+ <include refid="applyStudyViewFilter">
+ <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+ </include>
  AND gpg.gene = #{genomicDataFilter.hugoGeneSymbol}
  AND sgp.alteration_type = 'MUTATION_EXTENDED'
  ),
  mutated_count as (
  SELECT count(distinct sample_unique_id)
  FROM genomic_event_derived
- WHERE sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
+ WHERE
+ <include refid="applyStudyViewFilter">
+ <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+ </include>
  AND hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
  AND variant_type = 'mutation'
  )
@@ -309,7 +316,9 @@
  count(distinct(sample_unique_id)) as uniqueCount
  FROM genomic_event_derived
  <where>
- sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>)
+ <include refid="applyStudyViewFilter">
+ <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+ </include>
  AND variant_type = 'mutation'
  <foreach item="genomicDataFilter" collection="genomicDataFilters" open=" AND (" separator=" OR " close=")">
  hugo_gene_symbol = #{genomicDataFilter.hugoGeneSymbol}
@@ -595,10 +604,9 @@
  SELECT * FROM genomic_numerical_query
  UNION ALL
  SELECT
- attributeId,
+ coalesce((SELECT attributeId FROM genomic_numerical_sum LIMIT 1), concat(#{genomicDataBinFilters[0].hugoGeneSymbol}, #{profileType})) as attributeId,
  'NA' as value,
- cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - genomic_numerical_count) as INTEGER) as count
- FROM genomic_numerical_sum
+ cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - coalesce((SELECT genomic_numerical_count FROM genomic_numerical_sum LIMIT 1), 0)) as INTEGER) as count
  </select>
 
  <select id="getGenericAssayDataBinCounts" resultType="org.cbioportal.model.ClinicalDataCount">