From 692f34c54a8e298646b74c43b2ee883c37c870b1 Mon Sep 17 00:00:00 2001
From: Gaofei Zhao <15748980+dippindots@users.noreply.github.com>
Date: Thu, 29 Aug 2024 01:46:24 -0400
Subject: [PATCH] code cleanup

---
 .../java/org/cbioportal/web/columnar/BasicDataBinner.java  | 7 +++----
 src/main/resources/db-scripts/clickhouse/clickhouse.sql    | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java
index 05f3c79944e..f47beb9f9b6 100644
--- a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java
+++ b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java
@@ -67,12 +67,11 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
 
         // we need to fetch data for the partial filter in order to generate the bins for initial state
         // we use the filtered data to calculate the counts for each bin, we do not regenerate bins for the filtered data
-        // TODO: update this before review, should create a function for this
         List<ClinicalDataCountItem> unfilteredClinicalDataCounts;
         List<ClinicalDataCountItem> filteredClinicalDataCounts;
         Map<String, ClinicalDataType> attributeDatatypeMap;
         switch (dataBinCountFilter) {
-            // TODO: this is to support clinical data, but clinical data is not using this now. We should update controller to use this method later
+            // TODO: first case is to support clinical data, but clinical data is not using this now. We should update controller to use this method later
             case ClinicalDataBinCountFilter clinicalDataBinCountFilter -> {
                 unfilteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(partialFilter, uniqueKeys);
                 filteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, uniqueKeys);
@@ -112,7 +111,7 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
         // Define result variables
         List<U> resultDataBins = Collections.emptyList();
 
-        // TODO: need to update attributeDatatypeMap to ignore patient level data
+        // TODO: need to update attributeDatatypeMap to include patient level data for Generic Assay Profiles
         if (dataBinMethod == DataBinMethod.STATIC) {
             if (!unfilteredClinicalData.isEmpty()) {
                 resultDataBins = calculateStaticDataBins(
@@ -124,7 +123,7 @@ public <T extends DataBinCountFilter, S extends DataBinFilter, U extends DataBin
                 );
             }
         }
-        // TODO: need to update attributeDatatypeMap to ignore patient level data
+        // TODO: need to update attributeDatatypeMap to include patient level data for Generic Assay Profiles
         else { // dataBinMethod == DataBinMethod.DYNAMIC
             // TODO we should consider removing dynamic binning support
             //  we never use dynamic binning in the frontend because number of bins and the bin ranges can change 
diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
index 990b958e85f..ffb18b1979d 100644
--- a/src/main/resources/db-scripts/clickhouse/clickhouse.sql
+++ b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
@@ -435,4 +435,4 @@ OPTIMIZE TABLE clinical_data_derived;
 OPTIMIZE TABLE clinical_event_derived;
 OPTIMIZE TABLE genetic_alteration_cna_derived;
 OPTIMIZE TABLE genetic_alteration_numerical_derived;
-OPTIMIZE TABLE generic_assay_data_derived;
\ No newline at end of file
+OPTIMIZE TABLE generic_assay_data_derived;