From b58a18c25b93dcf6250b94a1680180492be833fe Mon Sep 17 00:00:00 2001 From: Charles Haynes <33608920+haynescd@users.noreply.github.com> Date: Tue, 8 Oct 2024 13:04:06 -0400 Subject: [PATCH] Rfc80/add na clinical data filtering (#11050) * Add Categorical Clinical Attribute NA filtering * add api tests --------- Co-authored-by: alisman --- .../StudyViewFilterMapper.xml | 96 +++++++++++++++--- test/api-e2e/specs/clinical-data-filters.json | 99 ++++++++++++++++++- 2 files changed, 181 insertions(+), 14 deletions(-) diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index b1e179be264..1ff28729b63 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -317,6 +317,46 @@ + + + + + + + + + + + + + + + ( + + + SELECT DISTINCT ${unique_id} + FROM sample_derived sd + LEFT JOIN () AS categorical_clinical_data + ON + + + sd.sample_unique_id = categorical_clinical_data.sample_unique_id + + + sd.patient_unique_id = categorical_clinical_data.patient_unique_id + + + WHERE empty(attribute_value) + AND EXISTS () + + + + + UNION ALL + + + + SELECT ${unique_id} FROM ${table_name} WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND @@ -368,23 +408,53 @@ + + ) - - SELECT ${unique_id} - FROM ${table_name} - WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND - type='${type}' - - - AND ( - - - - ) ILIKE '${dataFilterValue.value}' - + + SELECT sample_unique_id, patient_unique_id, attribute_value + FROM clinical_data_derived + WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND type='${type}' + AND cancer_study_identifier IN + + #{studyId} + + + + ( + SELECT ${unique_id} + FROM sample_derived sd + LEFT JOIN () AS categorical_clinical_data + ON + + + sd.sample_unique_id = categorical_clinical_data.sample_unique_id + + + sd.patient_unique_id = categorical_clinical_data.patient_unique_id + + + WHERE + + + + empty(attribute_value) + + + ( + + + + ) ILIKE '${dataFilterValue.value}' + + + + AND EXISTS () + ) + diff --git a/test/api-e2e/specs/clinical-data-filters.json b/test/api-e2e/specs/clinical-data-filters.json index 2c6614d99d6..b11a6ae46b8 100644 --- a/test/api-e2e/specs/clinical-data-filters.json +++ b/test/api-e2e/specs/clinical-data-filters.json @@ -3585,5 +3585,102 @@ } ] - } + }, + { + "name":"combined study with NA filtering", + "note":"tests that filtering for null values in combined study scenario", + "studies":["acc_tcga_pan_can_atlas_2018","nsclc_public_genie_bpc"], + "tests":[ + {"hash":116543724,"filterString":"Diagnosis Age:> 35Ethnicity 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