From deaec52a1e8b479fdfe8e6e668ef915c976c58a7 Mon Sep 17 00:00:00 2001 From: Gaofei Zhao Date: Tue, 14 Oct 2025 15:17:50 -0400 Subject: [PATCH 1/3] Fix sample list query for clickhouse --- .../persistence/mybatis/SampleListMapper.xml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml index bb990d81d8b..87905f86fe8 100644 --- a/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml @@ -4,16 +4,15 @@ - - ANY_VALUE(sample_list.list_id) AS "${prefix}listId", - ANY_VALUE(sample_list.stable_id) AS "${prefix}stableId" + sample_list.list_id AS "${prefix}listId", + sample_list.stable_id AS "${prefix}stableId" , - 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 "${prefix}description" + sample_list.cancer_study_id AS "${prefix}cancerStudyId", + cancer_study.cancer_study_identifier AS "${prefix}cancerStudyIdentifier", + sample_list.category AS "${prefix}category", + sample_list.name AS "${prefix}name", + sample_list.description AS "${prefix}description" , From 9ba8899ee86872f039830d4014b80e09fe111d5a Mon Sep 17 00:00:00 2001 From: Gaofei Zhao Date: Tue, 14 Oct 2025 15:52:49 -0400 Subject: [PATCH 2/3] Change cancer study details query in sample list query --- .../legacy/persistence/mybatis/SampleListMapper.xml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml index 87905f86fe8..f7c79bfeb7a 100644 --- a/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml @@ -16,9 +16,16 @@ , - - - + cancer_study.type_of_cancer_id AS "${prefix}cancerStudy.typeOfCancerId", + cancer_study.name AS "${prefix}cancerStudy.name", + cancer_study.description AS "${prefix}cancerStudy.description", + cancer_study.public AS "${prefix}cancerStudy.publicStudy", + cancer_study.pmid AS "${prefix}cancerStudy.pmid", + cancer_study.citation AS "${prefix}cancerStudy.citation", + cancer_study.groups AS "${prefix}cancerStudy.groups", + cancer_study.status AS "${prefix}cancerStudy.status", + cancer_study.import_date AS "${prefix}cancerStudy.importDate", + reference_genome.name AS "${prefix}cancerStudy.referenceGenome" From b5a9ee8cadefd51d3f7b41f0a1ef436f70aab63d Mon Sep 17 00:00:00 2001 From: Gaofei Zhao Date: Fri, 17 Oct 2025 01:28:53 -0400 Subject: [PATCH 3/3] Clean up SampleListMapper.xml by removing unused prefix properties --- .../persistence/mybatis/SampleListMapper.xml | 46 ++++++++----------- 1 file changed, 20 insertions(+), 26 deletions(-) diff --git a/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml index f7c79bfeb7a..c66ba62046f 100644 --- a/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml +++ b/src/main/resources/org/cbioportal/legacy/persistence/mybatis/SampleListMapper.xml @@ -4,36 +4,34 @@ - sample_list.list_id AS "${prefix}listId", - sample_list.stable_id AS "${prefix}stableId" + sample_list.list_id AS "listId", + sample_list.stable_id AS "stableId" , - sample_list.cancer_study_id AS "${prefix}cancerStudyId", - cancer_study.cancer_study_identifier AS "${prefix}cancerStudyIdentifier", - sample_list.category AS "${prefix}category", - sample_list.name AS "${prefix}name", - sample_list.description AS "${prefix}description" + sample_list.cancer_study_id AS "cancerStudyId", + cancer_study.cancer_study_identifier AS "cancerStudyIdentifier", + sample_list.category AS "category", + sample_list.name AS "name", + sample_list.description AS "description" , - cancer_study.type_of_cancer_id AS "${prefix}cancerStudy.typeOfCancerId", - cancer_study.name AS "${prefix}cancerStudy.name", - cancer_study.description AS "${prefix}cancerStudy.description", - cancer_study.public AS "${prefix}cancerStudy.publicStudy", - cancer_study.pmid AS "${prefix}cancerStudy.pmid", - cancer_study.citation AS "${prefix}cancerStudy.citation", - cancer_study.groups AS "${prefix}cancerStudy.groups", - cancer_study.status AS "${prefix}cancerStudy.status", - cancer_study.import_date AS "${prefix}cancerStudy.importDate", - reference_genome.name AS "${prefix}cancerStudy.referenceGenome" + 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" 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 @@ -80,9 +76,7 @@