From d46400fefc4da257c4f75cb9db2c505c01e5fc66 Mon Sep 17 00:00:00 2001
From: Bryan Lai <laib1@mskcc.org>
Date: Tue, 6 Aug 2024 18:09:45 -0400
Subject: [PATCH] add comments to filter sql

---
 .../StudyViewFilterMapper.xml                 | 61 +++++++++----------
 1 file changed, 28 insertions(+), 33 deletions(-)

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
index b98b4a5690e..1a3897d98e7 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -66,49 +66,44 @@
                     '${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
                 </foreach>
             </if>
-            <!-- custom data filter -->
             <if test="studyViewFilter.customDataFilters != null and !studyViewFilter.customDataFilters.isEmpty() and customDataSamples != null">
                 INTERSECT
                 SELECT sample_unique_id
                 FROM sample_derived
-                <!-- customDataSamples are samples filtered based on the customDataFilters -->
-                <!-- filter for samples in customDataSamples if customDataSamples isn't empty, else all samples are filtered out -->
-                <choose>
-                    <when test="!customDataSamples.isEmpty()">
-                        WHERE
-                        <trim prefix="" prefixOverrides="AND">
-                            <foreach item="customDataFilter" collection="studyViewFilter.customDataFilters">
-                                AND
-                                (
-                                    sample_unique_id IN (
-                                        '',
+                WHERE
+                <trim prefix="" prefixOverrides="AND">
+                    <!-- filter for samples that pass all customDataFilters (using AND logic on samples passing each filter) -->
+                    <foreach item="customDataFilter" collection="studyViewFilter.customDataFilters">
+                        AND
+                        (
+                            <!-- filter for samples that pass the customDataFilter excluding NA logic -->
+                            <!-- samples pass the customDataFilter if they are not filtered out (getIsFilteredOut() is false) -->
+                            <!-- in the event customDataSamples is empty, all samples are filtered out -->
+                            sample_unique_id IN (
+                                '',
+                                <foreach item="sampleIdentifier" collection="customDataSamples" separator=",">
+                                    <if test="customDataFilter.attributeId == sampleIdentifier.getAttributeId() and !sampleIdentifier.getIsFilteredOut()">
+                                        '${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
+                                    </if>
+                                </foreach>
+                            )
+                            <!-- if customDataFilter contains NA value, filter for samples that are not in the user submitted custom list (customDataSamples) -->
+                            <!-- use OR logic to get the samples that pass the NA or non-NA logic of the customDataFilter -->
+                            <foreach item="customDataFilterValue" collection="customDataFilter.values">
+                                <if test="customDataFilterValue.value eq 'NA'">
+                                    OR
+                                    sample_unique_id NOT IN (
                                         <foreach item="sampleIdentifier" collection="customDataSamples" separator=",">
-                                            <if test="customDataFilter.attributeId == sampleIdentifier.getAttributeId() and !sampleIdentifier.getIsFilteredOut()">
+                                            <if test="customDataFilter.attributeId == sampleIdentifier.getAttributeId()">
                                                 '${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
                                             </if>
                                         </foreach>
                                     )
-                                    <foreach item="customDataFilterValue" collection="customDataFilter.values">
-                                        <if test="customDataFilterValue.value eq 'NA'">
-                                            OR
-                                            sample_unique_id NOT IN (
-                                            '',
-                                            <foreach item="sampleIdentifier" collection="customDataSamples" separator=",">
-                                                <if test="customDataFilter.attributeId == sampleIdentifier.getAttributeId()">
-                                                    '${sampleIdentifier.studyId}_${sampleIdentifier.sampleId}'
-                                                </if>
-                                            </foreach>
-                                            )
-                                        </if>
-                                    </foreach>
-                                )
+                                </if>
                             </foreach>
-                        </trim>
-                    </when>
-                    <otherwise>
-                        ''
-                    </otherwise>
-                </choose>
+                        )
+                    </foreach>
+                </trim>
             </if>
             <if test="studyViewFilter.geneFilters != null and !studyViewFilter.geneFilters.isEmpty()">
                 <foreach item="profileGroup" collection="studyViewFilter.geneFilters">