From 4ec81bc63d9bf9f2f5a54dbf2f9ee9af1cb0ab3a Mon Sep 17 00:00:00 2001
From: Charles Haynes <haynescd@chop.edu>
Date: Tue, 27 Aug 2024 16:23:48 -0400
Subject: [PATCH 1/2] Update Treatment Endpoint to handle event_type TREATMENT,
 previously only searched on Treatment

---
 .../mybatisclickhouse/StudyViewFilterMapper.xml           | 6 +++---
 .../persistence/mybatisclickhouse/StudyViewMapper.xml     | 8 ++++----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
index c0b2909cd53..7ec8f970f92 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -189,8 +189,8 @@
                     value AS treatment,
                     argMin(start_date, start_date) AS treatment_time_taken
                 FROM clinical_event_derived
-                WHERE event_type = 'Treatment'
-                AND key = 'AGENT'
+                WHERE event_type IN ('Treatment', 'TREATMENT')
+            AND key = 'AGENT'
                 GROUP BY patient_unique_id, value
             ) ced_inner ON ced_inner.patient_unique_id = ced.patient_unique_id
             <where>
@@ -231,7 +231,7 @@
             <where>
                 <foreach item="patientTreatmentFilter" collection="andedPatientTreatmentFilters.getFilters()" open="(" separator=") OR ("
                          close=")">
-                    event_type = 'Treatment'
+                    event_type IN ('Treatment', 'TREATMENT')
                     AND key = 'AGENT'
                     AND value = '${patientTreatmentFilter.treatment}'
                 </foreach>
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
index e94d466f6f0..7571d5f9870 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -442,7 +442,7 @@
                     patient_unique_id
                 FROM clinical_event_derived
                 <where>
-                    event_type = 'Treatment'
+                    event_type IN ('Treatment', 'TREATMENT')
                     AND key = 'AGENT'
                     AND
                     <include refid="applyStudyViewFilter">
@@ -465,7 +465,7 @@
         count(DISTINCT patient_unique_id) AS count
         FROM clinical_event_derived
         <where>
-            event_type = 'Treatment'
+            event_type IN ('Treatment', 'TREATMENT')
             AND key = 'AGENT'
             AND
             <include refid="applyStudyViewFilter">
@@ -493,7 +493,7 @@
                 patient_unique_id
             FROM clinical_event_derived
             <where>
-                event_type = 'Treatment'
+                event_type IN ('Treatment', 'TREATMENT')
                 AND key = 'AGENT'
                 AND
                 <include refid="applyStudyViewFilter">
@@ -537,7 +537,7 @@
                 argMin(start_date, start_date) AS treatment_time_taken
             FROM clinical_event_derived
             <where>
-                event_type = 'Treatment'
+                event_type IN ('Treatment', 'TREATMENT')
                 AND key = 'AGENT'
             </where>
             GROUP BY patient_unique_id, value

From 1bcb80b1f0adc1f283201e924d73f2ddf9f7f389 Mon Sep 17 00:00:00 2001
From: Charles Haynes <haynescd@chop.edu>
Date: Tue, 27 Aug 2024 16:46:05 -0400
Subject: [PATCH 2/2] Handle all variations of Treatment

---
 .../mybatisclickhouse/StudyViewFilterMapper.xml           | 6 +++---
 .../persistence/mybatisclickhouse/StudyViewMapper.xml     | 8 ++++----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
index 7ec8f970f92..f2ce040188e 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -189,8 +189,8 @@
                     value AS treatment,
                     argMin(start_date, start_date) AS treatment_time_taken
                 FROM clinical_event_derived
-                WHERE event_type IN ('Treatment', 'TREATMENT')
-            AND key = 'AGENT'
+                WHERE lower(event_type) = 'treatment'
+                AND key = 'AGENT'
                 GROUP BY patient_unique_id, value
             ) ced_inner ON ced_inner.patient_unique_id = ced.patient_unique_id
             <where>
@@ -231,7 +231,7 @@
             <where>
                 <foreach item="patientTreatmentFilter" collection="andedPatientTreatmentFilters.getFilters()" open="(" separator=") OR ("
                          close=")">
-                    event_type IN ('Treatment', 'TREATMENT')
+                    lower(event_type) = 'treatment'
                     AND key = 'AGENT'
                     AND value = '${patientTreatmentFilter.treatment}'
                 </foreach>
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
index 7571d5f9870..5af781dfeb0 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -442,7 +442,7 @@
                     patient_unique_id
                 FROM clinical_event_derived
                 <where>
-                    event_type IN ('Treatment', 'TREATMENT')
+                    lower(event_type) = 'treatment'
                     AND key = 'AGENT'
                     AND
                     <include refid="applyStudyViewFilter">
@@ -465,7 +465,7 @@
         count(DISTINCT patient_unique_id) AS count
         FROM clinical_event_derived
         <where>
-            event_type IN ('Treatment', 'TREATMENT')
+            lower(event_type) = 'treatment'
             AND key = 'AGENT'
             AND
             <include refid="applyStudyViewFilter">
@@ -493,7 +493,7 @@
                 patient_unique_id
             FROM clinical_event_derived
             <where>
-                event_type IN ('Treatment', 'TREATMENT')
+                lower(event_type) = 'treatment'
                 AND key = 'AGENT'
                 AND
                 <include refid="applyStudyViewFilter">
@@ -537,7 +537,7 @@
                 argMin(start_date, start_date) AS treatment_time_taken
             FROM clinical_event_derived
             <where>
-                event_type IN ('Treatment', 'TREATMENT')
+                lower(event_type) = 'treatment'
                 AND key = 'AGENT'
             </where>
             GROUP BY patient_unique_id, value