remove duplicate code

cBioPortal · Jul 7, 2023 · 4fa24f1 · 4fa24f1
1 parent 9178c29
commit 4fa24f1
Showing 1 changed file with 15 additions and 31 deletions.
diff --git a/...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml b/...atis/src/main/resources/org/cbioportal/persistence/mybatiscolumnstore/StudyViewMapper.xml
@@ -46,16 +46,20 @@
 
     <!-- for /clinical-data-counts/fetch (returns ClinicalData) which will then be converted to clinicalDataCountItems -->
     <select id="getClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
-      <include refid="getPatientClinicalDataCountsQuery"/>
+        <include refid="getCategoricalClinicalDataCountsQuery">
+            <property name="table_name_prefix" value="patient"/>
+        </include>
         UNION ALL
-        <include refid="getSampleClinicalDataCountsQuery"/>
+        <include refid="getCategoricalClinicalDataCountsQuery">
+            <property name="table_name_prefix" value="sample"/>
+        </include>
     </select>
-    <sql id="getPatientClinicalDataCountsQuery">
+    <sql id="getCategoricalClinicalDataCountsQuery">
         SELECT
         attribute_name as attributeId,
         CASE WHEN attribute_value = 'NULL' THEN 'NA' ELSE attribute_value END AS value,
         Count(*) as count
-        FROM patient_clinical_attribute_categorical
+        FROM ${table_name_prefix}_clinical_attribute_categorical
         <where>
             patient_unique_id IN ( <include refid="getPatientIdsFromSampleIdFilters"/>
             <if test="applyPatientIdFilters == true">
@@ -72,38 +76,18 @@
             </foreach>
         </where>
         GROUP BY attribute_name,
-        attribute_value 
+        attribute_value
     </sql>
     <select id="getPatientClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
-        <include refid="getPatientClinicalDataCountsQuery"/>
+        <include refid="getCategoricalClinicalDataCountsQuery">
+            <property name="table_name_prefix" value="patient"/>
+        </include>
     </select>
     <select id="getSampleClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
-        <include refid="getSampleClinicalDataCountsQuery"/>
+        <include refid="getCategoricalClinicalDataCountsQuery">
+            <property name="table_name_prefix" value="sample"/>
+        </include>
     </select>
-    <sql id="getSampleClinicalDataCountsQuery">
-        SELECT
-        attribute_name as attributeId,
-        CASE WHEN attribute_value = 'NULL' THEN 'NA' ELSE attribute_value END AS value,
-        Count(*) as count
-        FROM sample_clinical_attribute_categorical
-        <where>
-            patient_unique_id IN ( <include refid="getPatientIdsFromSampleIdFilters"/>
-            <if test="applyPatientIdFilters == true">
-                INTERSECT <include refid="patientUniqueIdsFromStudyViewFilter"/>
-            </if>
-            )
-            AND UPPER(attribute_value) NOT IN
-            <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">
-                #{filteredAttributeValue}
-            </foreach>
-            AND attribute_name IN
-            <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
-                #{attributeId}
-            </foreach>
-        </where>
-        GROUP BY attribute_name,
-        attribute_value
-    </sql>
 
     <!-- This block represents the Study View Filter -->
     <sql id="sampleUniqueIdsFromStudyViewFilter">