Rfc80/add na clinical data filtering (#11050)

* Add Categorical Clinical Attribute NA filtering * add api tests --------- Co-authored-by: alisman <[email protected]>
cBioPortal · Nov 24, 2024 · 29be4af · 29be4af
1 parent 2f48ea7
commit 29be4af
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diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -317,6 +317,46 @@
     </sql>
 
     <sql id="numericalClinicalDataCountFilter">
+
+        <!-- check if 'NA' is selected -->
+        <bind name="userSelectsNA" value="false" />
+        <bind name="userSelectsNumericalValue" value="false" />
+        <foreach item="dataFilterValue" collection="clinicalDataFilter.values">
+            <choose>
+                <when test="dataFilterValue.value == 'NA'">
+                    <bind name="userSelectsNA" value="true" />
+                </when>
+                <otherwise>
+                    <bind name="userSelectsNumericalValue" value="true" />
+                </otherwise>
+            </choose>
+        </foreach>
+        (
+        <!-- if 'NA' is selected, prepare NA samples -->
+        <if test="userSelectsNA">
+            SELECT DISTINCT ${unique_id}
+            FROM sample_derived sd
+            LEFT JOIN (<include refid="selectAllClinicalDataByAttribute"/>) AS categorical_clinical_data
+            ON
+            <choose>
+                <when test="'${type}' == 'sample'">
+                    sd.sample_unique_id = categorical_clinical_data.sample_unique_id
+                </when>
+                <otherwise>
+                    sd.patient_unique_id = categorical_clinical_data.patient_unique_id
+                </otherwise>
+            </choose>
+            WHERE empty(attribute_value)
+            AND EXISTS (<include refid="selectAllClinicalDataByAttribute"/>)
+        </if>
+
+        <!-- if both 'NA' and non-NA are selected, union them together -->
+        <if test="userSelectsNA and userSelectsNumericalValue">
+            UNION ALL
+        </if>
+
+        <!-- if non-NA is selected, prepare non-NA samples -->
+        <if test="userSelectsNumericalValue">
         SELECT ${unique_id}
         FROM ${table_name}
         WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND
@@ -368,23 +408,53 @@
                 </if>
             </trim>
         </foreach>
+        </if>
+        )
     </sql>
 
-    <sql id="categoricalClinicalDataCountFilter">
-        SELECT ${unique_id}
-        FROM ${table_name}
-        WHERE attribute_name = '${clinicalDataFilter.attributeId}' AND
-        type='${type}'
-        <foreach item="dataFilterValue" collection="clinicalDataFilter.values" open=" AND ((" separator=") OR (" close="))">
-            <trim prefix="" prefixOverrides="AND">
-                AND (
-                    <include refid="normalizeAttributeValue">
-                        <property name="attribute_value" value="attribute_value"/>
-                    </include>
-                ) ILIKE '${dataFilterValue.value}'
-            </trim>
+    <sql id="selectAllClinicalDataByAttribute">
+        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
+        <foreach item="studyId" collection="studyViewFilterHelper.studyViewFilter.studyIds" open="(" separator="," close=")">
+            #{studyId}
+
         </foreach>
     </sql>
+
+    <sql id="categoricalClinicalDataCountFilter">
+        (
+            SELECT ${unique_id}
+            FROM sample_derived sd
+            LEFT JOIN (<include refid="selectAllClinicalDataByAttribute"/>) AS categorical_clinical_data
+            ON
+            <choose>
+                <when test="'${type}' == 'sample'">
+                    sd.sample_unique_id = categorical_clinical_data.sample_unique_id
+                </when>
+                <otherwise>
+                    sd.patient_unique_id = categorical_clinical_data.patient_unique_id
+                </otherwise>
+            </choose>
+            WHERE
+            <foreach item="dataFilterValue" collection="clinicalDataFilter.values" open=" ((" separator=") OR (" close="))">
+                <choose>
+                    <when test="dataFilterValue.value == 'NA'">
+                        empty(attribute_value)
+                    </when>
+                    <otherwise>
+                        (
+                        <include refid="normalizeAttributeValue">
+                            <property name="attribute_value" value="attribute_value"/>
+                        </include>
+                        ) ILIKE '${dataFilterValue.value}'
+                    </otherwise>
+                </choose> 
+            </foreach> 
+            AND EXISTS (<include refid="selectAllClinicalDataByAttribute"/>)
+        )
+    </sql>
 
     <sql id="numericalGenomicDataFilter">
         <!-- check if 'NA' is selected -->