Generate new generic assay table with NA values represented

alisman · Sep 3, 2024 · 6b4d625 · 6b4d625
1 parent 030e7f1
commit 6b4d625
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Showing 3 changed files with 28 additions and 3 deletions.
diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
@@ -365,6 +365,7 @@ FROM
     ) AS subquery
         JOIN sample_derived sd ON sd.internal_id = subquery.sample_id;
 
+-- defunct
 CREATE TABLE IF NOT EXISTS generic_assay_data_derived
 (
     sample_unique_id String,
@@ -380,6 +381,30 @@ CREATE TABLE IF NOT EXISTS generic_assay_data_derived
     ENGINE = MergeTree()
     ORDER BY (profile_type, entity_stable_id, sample_unique_id);
 
+-- this handles NAs
+INSERT INTO TABLE generic_assay_data_derivedNEW
+SELECT sd.sample_unique_id as sample_unique_id,
+       ga.genetic_entity_id as genetic_entity_id,
+       multiIf(gadd.value='', 'NA', gadd.value=NULL, 'NA', gadd.value) as value,
+       gp.generic_assay_type as generic_assay_type,
+       gp.stable_id as profile_stable_id,
+       ge.stable_id as entity_stable_id,
+       gp.datatype as datatype,
+       gp.patient_level as patient_level,
+       replaceOne(gp.stable_id, concat(cs.cancer_study_identifier, '_'), '') as profile_type
+FROM genetic_alteration ga
+         LEFT JOIN genetic_profile gp on ga.genetic_profile_id = gp.genetic_profile_id
+         LEFT JOIN genetic_entity ge on ga.genetic_entity_id = ge.id
+         LEFT JOIN cancer_study cs on cs.cancer_study_id = gp.cancer_study_id
+         RIGHT JOIN sample_derived sd on cs.cancer_study_identifier = sd.cancer_study_identifier
+         LEFT JOIN generic_assay_data_derivedAA gadd ON
+            gadd.sample_unique_id=sd.sample_unique_id
+        AND gadd.entity_stable_id = ge.stable_id
+        AND gadd.profile_stable_id = gp.stable_id
+
+WHERE cs.cancer_study_identifier='prad_tcga_pan_can_atlas_2018'
+
+
 INSERT INTO TABLE generic_assay_data_derived
 SELECT
     sd.sample_unique_id as sample_unique_id,

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -173,15 +173,15 @@
                 <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
                     <include refid="numericalGenericAssayDataCountFilter">
                         <property name="unique_id" value="sample_unique_id"/>
-                        <property name="table_name" value="generic_assay_data_derived"/>
+                        <property name="table_name" value="generic_assay_data_derivedNEW"/>
                     </include>
                 </foreach>
             </if>
             <if test="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters() != null and !studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters().isEmpty()">
                 <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
                     <include refid="categoricalGenericAssayDataCountFilter">
                         <property name="unique_id" value="sample_unique_id"/>
-                        <property name="table_name" value="generic_assay_data_derived"/>
+                        <property name="table_name" value="generic_assay_data_derivedNEW"/>
                     </include>
                 </foreach>
             </if>

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -585,7 +585,7 @@
             <property name="attribute_value" value="value"/>
         </include> AS value,
         count(value) AS count
-        FROM generic_assay_data_derived
+        FROM generic_assay_data_derivedNEW
         <where>
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>