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Fix sample list error (clickhouse-only) #11753

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Merged
merged 3 commits into from
Oct 17, 2025
Merged

Fix sample list error (clickhouse-only) #11753

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deaec52
Fix sample list query for clickhouse
dippindots Oct 14, 2025
9ba8899
Change cancer study details query in sample list query
dippindots Oct 14, 2025
b5a9ee8
Clean up SampleListMapper.xml by removing unused prefix properties
dippindots Oct 17, 2025
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40 changes: 20 additions & 20 deletions src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,30 +4,34 @@
<mapper namespace="org.cbioportal.legacy.persistence.mybatis.SampleListMapper">

<sql id="select">
<!-- ROB: TODO : there is no GROUP BY clause in this file, so why were these problems? -->
ANY_VALUE(sample_list.list_id) AS "${prefix}listId",
ANY_VALUE(sample_list.stable_id) AS "${prefix}stableId"
sample_list.list_id AS "listId",
sample_list.stable_id AS "stableId"
<if test="projection == 'SUMMARY' || projection == 'DETAILED'">
,
ANY_VALUE(sample_list.cancer_study_id) AS "${prefix}cancerStudyId",
ANY_VALUE(cancer_study.cancer_study_identifier) AS "${prefix}cancerStudyIdentifier",
ANY_VALUE(sample_list.category) AS "${prefix}category",
ANY_VALUE(sample_list.name) AS "${prefix}name",
ANY_VALUE(sample_list.description) AS "${prefix}description"
sample_list.cancer_study_id AS "cancerStudyId",
cancer_study.cancer_study_identifier AS "cancerStudyIdentifier",
sample_list.category AS "category",
sample_list.name AS "name",
sample_list.description AS "description"
</if>
<if test="projection == 'DETAILED'">
,
<include refid="org.cbioportal.legacy.persistence.mybatis.StudyMapper.select">
<property name="prefix" value="${prefix}cancerStudy."/>
</include>
cancer_study.type_of_cancer_id AS "cancerStudy.typeOfCancerId",
cancer_study.name AS "cancerStudy.name",
cancer_study.description AS "cancerStudy.description",
cancer_study.public AS "cancerStudy.publicStudy",
cancer_study.pmid AS "cancerStudy.pmid",
cancer_study.citation AS "cancerStudy.citation",
cancer_study.groups AS "cancerStudy.groups",
cancer_study.status AS "cancerStudy.status",
cancer_study.import_date AS "cancerStudy.importDate",
reference_genome.name AS "cancerStudy.referenceGenome"
</if>
</sql>

<select id="getAllSampleLists" resultType="org.cbioportal.legacy.model.SampleList">
SELECT
<include refid="select">
<property name="prefix" value=""/>
</include>
<include refid="select"/>
FROM sample_list
INNER JOIN cancer_study ON sample_list.cancer_study_id = cancer_study.cancer_study_id
INNER JOIN reference_genome ON cancer_study.reference_genome_id = reference_genome.reference_genome_id
Expand Down Expand Up @@ -63,9 +67,7 @@

<select id="getSampleList" resultType="org.cbioportal.legacy.model.SampleList">
SELECT
<include refid="select">
<property name="prefix" value=""/>
</include>
<include refid="select"/>
FROM sample_list
INNER JOIN cancer_study ON sample_list.cancer_study_id = cancer_study.cancer_study_id
INNER JOIN reference_genome ON cancer_study.reference_genome_id = reference_genome.reference_genome_id
Expand All @@ -74,9 +76,7 @@

<select id="getSampleLists" resultType="org.cbioportal.legacy.model.SampleList">
SELECT
<include refid="select">
<property name="prefix" value=""/>
</include>
<include refid="select"/>
FROM sample_list
INNER JOIN cancer_study ON sample_list.cancer_study_id = cancer_study.cancer_study_id
INNER JOIN reference_genome ON cancer_study.reference_genome_id = reference_genome.reference_genome_id
Expand Down
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