Update generic assay table schema

cBioPortal · Nov 11, 2024 · f59044a · f59044a
1 parent 3f7b42f
commit f59044a
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Showing 3 changed files with 5 additions and 7 deletions.
diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
@@ -333,13 +333,13 @@ FROM
 CREATE TABLE IF NOT EXISTS generic_assay_data_derived
 (
     sample_unique_id String,
+    patient_unique_id String,
     genetic_entity_id String,
     value String,
     generic_assay_type String,
     profile_stable_id String,
     entity_stable_id String,
     datatype String,
-    patient_level NUMERIC,
     profile_type String
 )
     ENGINE = MergeTree()
@@ -348,13 +348,13 @@ CREATE TABLE IF NOT EXISTS generic_assay_data_derived
 INSERT INTO TABLE generic_assay_data_derived
 SELECT
     sd.sample_unique_id as sample_unique_id,
+    sd.patient_unique_id as patient_unique_id,
     genetic_entity_id,
     value,
     generic_assay_type,
     profile_stable_id,
     entity_stable_id,
     datatype,
-    patient_level,
     replaceOne(profile_stable_id, concat(cs.cancer_study_identifier, '_'), '') as profile_type
 FROM
     (SELECT
@@ -366,7 +366,6 @@ FROM
          genetic_profile_id,
          profile_stable_id,
          entity_stable_id,
-         patient_level,
          datatype
      FROM
          (SELECT
@@ -378,7 +377,6 @@ FROM
               gp.stable_id as profile_stable_id,
               ge.stable_id as entity_stable_id,
               gp.datatype as datatype,
-              gp.patient_level as patient_level,
               arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(substring(ga.values, 1, -1)))) AS value,
               arrayMap(x -> (x = '' ? NULL : toInt64(x)), splitByString(',', assumeNotNull(substring(gps.ordered_sample_list, 1, -1)))) AS sample_id
           FROM genetic_profile gp

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -565,7 +565,7 @@
 
     <sql id="selectAllGenericAssays">
         SELECT sample_unique_id, patient_unique_id, value, datatype
-        FROM generic_assay_data_derived_patient
+        FROM generic_assay_data_derived
         WHERE profile_type = #{genericAssayDataFilter.profileType}
             AND entity_stable_id = #{genericAssayDataFilter.stableId}
     </sql>

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -315,7 +315,7 @@
                 entity_stable_id AS stableId,
                 value,
                 cast(count(*) AS INTEGER) AS count
-            FROM generic_assay_data_derived_patient
+            FROM generic_assay_data_derived
             <where>
                 <!-- Table creation in clickhouse.sql has ensured no NA values but extra caution is always appreciated -->
                 <include refid="normalizeAttributeValue">
@@ -723,7 +723,7 @@
                     <property name="attribute_value" value="value"/>
                 </include> AS value,
                 cast(count(value) as INTEGER) AS count
-            FROM generic_assay_data_derived_patient
+            FROM generic_assay_data_derived
             <where>
                 <!-- Need to ensure no NA values -->
                 <include refid="normalizeAttributeValue">