From a5f1a39b6fe06842457b16759eb2f218934c4bbc Mon Sep 17 00:00:00 2001
From: Onur Sumer <s.onur.sumer@gmail.com>
Date: Tue, 10 Dec 2024 11:21:39 -0500
Subject: [PATCH 1/2] fix CNA query for genomic data filter

---
 .../persistence/mybatisclickhouse/StudyViewFilterMapper.xml   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
index 0839283a1d2..30f3c7557b4 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -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}
@@ -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}

From 43c2bbaab60e701b0a9216ad844409b94119f808 Mon Sep 17 00:00:00 2001
From: Onur Sumer <s.onur.sumer@gmail.com>
Date: Tue, 10 Dec 2024 12:27:29 -0500
Subject: [PATCH 2/2] rename one of the cna_query statements to cna_count_query
 to avoid table name clash

---
 .../persistence/mybatisclickhouse/StudyViewMapper.xml       | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
index d91ff582ffe..e140fd00b6d 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -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,
@@ -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 -->