From 06c8b4c0b48e497025a7f434359b067552b533e4 Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Mon, 7 Oct 2024 14:12:22 -0400 Subject: [PATCH 1/4] Add Categorical Clinical Attribute NA filtering --- .../StudyViewFilterMapper.xml | 71 ++++++++++++++++--- 1 file changed, 61 insertions(+), 10 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..90d1eb3ea4c 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -370,20 +370,71 @@ + + 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 ${table_name} - WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND - type='${type}' - - - AND ( + + + + + + + + + + + + + + ( + + + 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 + type='${type}' + + + AND ( - ) ILIKE '${dataFilterValue.value}' - - + ) ILIKE '${dataFilterValue.value}' + + + + ) From 84304f55872f95cc8cd7aeb4fdb7d2e5f4d23ebb Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Mon, 7 Oct 2024 14:26:15 -0400 Subject: [PATCH 2/4] Add Numerical Clinical Data NA Filtering --- .../StudyViewFilterMapper.xml | 57 ++++++++++++++++--- 1 file changed, 50 insertions(+), 7 deletions(-) diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index 90d1eb3ea4c..a6eb7bd9f21 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 @@ -368,9 +408,11 @@ + + ) - + SELECT sample_unique_id, patient_unique_id, attribute_value FROM clinical_data_derived WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND type='${type}' @@ -380,17 +422,18 @@ + - + - + @@ -399,7 +442,7 @@ SELECT DISTINCT ${unique_id} FROM sample_derived sd - LEFT JOIN () AS categorical_clinical_data + LEFT JOIN () AS categorical_clinical_data ON @@ -410,16 +453,16 @@ WHERE empty(attribute_value) - AND EXISTS () + AND EXISTS () - + UNION ALL - + SELECT ${unique_id} FROM ${table_name} WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND From 696b2c262a432adafe50da30f789a5be763e0dbe Mon Sep 17 00:00:00 2001 From: Charles Haynes Date: Tue, 8 Oct 2024 12:35:59 -0400 Subject: [PATCH 3/4] Remove Union --- .../StudyViewFilterMapper.xml | 56 ++++++------------- 1 file changed, 16 insertions(+), 40 deletions(-) diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml index a6eb7bd9f21..1ff28729b63 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml @@ -424,23 +424,8 @@ - - - - - - - - - - - - - ( - - - SELECT DISTINCT ${unique_id} + SELECT ${unique_id} FROM sample_derived sd LEFT JOIN () AS categorical_clinical_data ON @@ -452,31 +437,22 @@ sd.patient_unique_id = categorical_clinical_data.patient_unique_id - WHERE empty(attribute_value) + WHERE + + + + empty(attribute_value) + + + ( + + + + ) ILIKE '${dataFilterValue.value}' + + + AND EXISTS () - - - - - UNION ALL - - - - - SELECT ${unique_id} - FROM ${table_name} - WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND - type='${type}' - - - AND ( - - - - ) ILIKE '${dataFilterValue.value}' - - - ) From 7e303fd52a7eb602e73c0ab69d655f20b7bbfd04 Mon Sep 17 00:00:00 2001 From: alisman Date: Tue, 8 Oct 2024 12:47:27 -0400 Subject: [PATCH 4/4] Add api tests for clinical data NA filtering --- test/api-e2e/specs/clinical-data-filters.json | 99 ++++++++++++++++++- 1 file changed, 98 insertions(+), 1 deletion(-) 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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