From 19599f28c9e6ff15696b4af17b45b1528a71317f Mon Sep 17 00:00:00 2001
From: Onur Sumer <s.onur.sumer@gmail.com>
Date: Fri, 10 Jan 2025 15:21:21 -0500
Subject: [PATCH] make xy plot data cacheable (#11278)

---
 .../service/StudyViewColumnarService.java     |  2 ++
 .../impl/StudyViewColumnarServiceImpl.java    | 30 +++++++++++++++++++
 .../StudyViewColumnStoreController.java       |  8 ++---
 .../columnar/util/ClinicalDataXyPlotUtil.java | 16 +++-------
 4 files changed, 38 insertions(+), 18 deletions(-)

diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
index 4f13dc68f78..67ee1f9efe4 100644
--- a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
+++ b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -58,4 +58,6 @@ public interface StudyViewColumnarService {
     List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataBinFilter> genericAssayDataBinFilters);
     
     List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
+
+    List<ClinicalData> fetchClinicalDataForXyPlot(StudyViewFilter studyViewFilter, List<String> attributeIds, boolean shouldFilterNonEmptyClinicalData);
 }
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
index a048d860656..f827a33411f 100644
--- a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -34,7 +34,10 @@
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
+import static org.cbioportal.web.columnar.util.ClinicalDataXyPlotUtil.combineClinicalDataForXyPlot;
+
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -273,6 +276,33 @@ public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewF
         return studyViewRepository.getMutationCountsByType(createContext(studyViewFilter), genomicDataFilters);
     }
     
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)"
+    )
+    @Override
+    public List<ClinicalData> fetchClinicalDataForXyPlot(
+        StudyViewFilter studyViewFilter,
+        List<String> attributeIds,
+        boolean shouldFilterNonEmptyClinicalData
+    ) {
+        List<ClinicalData> sampleClinicalDataList = this.getSampleClinicalData(studyViewFilter, attributeIds);
+        List<ClinicalData> patientClinicalDataList = this.getPatientClinicalData(studyViewFilter, attributeIds);
+        List<Sample> samples = Collections.emptyList();
+
+        if (!patientClinicalDataList.isEmpty()) {
+            // fetch samples for the given study view filter.
+            // we need this to construct the complete patient to sample map. 
+            samples = this.getFilteredSamples(studyViewFilter);
+        }
+
+        return combineClinicalDataForXyPlot(
+            sampleClinicalDataList,
+            patientClinicalDataList,
+            samples,
+            shouldFilterNonEmptyClinicalData
+        );
+    }
     
     private StudyViewFilterContext createContext(StudyViewFilter studyViewFilter) {
         List<CustomSampleIdentifier> customSampleIdentifiers = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
index bff2f6c1e58..39fc7001b8b 100644
--- a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
+++ b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -73,8 +73,6 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import static org.cbioportal.web.columnar.util.ClinicalDataXyPlotUtil.fetchClinicalDataForXyPlot;
-
 @InternalApi
 @RestController()
 @RequestMapping("/api")
@@ -307,8 +305,7 @@ public ResponseEntity<DensityPlotData> fetchClinicalDataDensityPlot(
             .yAxisLogScale(yAxisLogScale)
             .build();
         
-        List<ClinicalData> combinedClinicalDataList = fetchClinicalDataForXyPlot(
-            studyViewColumnarService,
+        List<ClinicalData> combinedClinicalDataList = studyViewColumnarService.fetchClinicalDataForXyPlot(
             interceptedStudyViewFilter,
             List.of(xAxisAttributeId, yAxisAttributeId),
             false
@@ -369,8 +366,7 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(
                 .ifPresent(f->interceptedStudyViewFilter.getClinicalDataFilters().remove(f));
         }
 
-        List<ClinicalData> combinedClinicalDataList = fetchClinicalDataForXyPlot(
-            studyViewColumnarService,
+        List<ClinicalData> combinedClinicalDataList = studyViewColumnarService.fetchClinicalDataForXyPlot(
             interceptedStudyViewFilter,
             List.of(numericalAttributeId, categoricalAttributeId),
             true // filter out clinical data with empty attribute values due to Clickhouse migration
diff --git a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java b/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java
index aee3a04a485..58b2d1e9c4e 100644
--- a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java
+++ b/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java
@@ -2,8 +2,6 @@
 
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.Sample;
-import org.cbioportal.service.StudyViewColumnarService;
-import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -12,15 +10,13 @@
 import java.util.stream.Stream;
 
 public class ClinicalDataXyPlotUtil {
-    public static List<ClinicalData> fetchClinicalDataForXyPlot(
-        StudyViewColumnarService studyViewColumnarService,
-        StudyViewFilter studyViewFilter,
-        List<String> attributeIds,
+    public static List<ClinicalData> combineClinicalDataForXyPlot(
+        List<ClinicalData> sampleClinicalDataList,
+        List<ClinicalData> patientClinicalDataList,
+        List<Sample> samples,
         boolean shouldFilterNonEmptyClinicalData
     ) {
         List<ClinicalData> combinedClinicalDataList;
-        List<ClinicalData> sampleClinicalDataList = studyViewColumnarService.getSampleClinicalData(studyViewFilter, attributeIds);
-        List<ClinicalData> patientClinicalDataList = studyViewColumnarService.getPatientClinicalData(studyViewFilter, attributeIds);
 
         if (shouldFilterNonEmptyClinicalData) {
             sampleClinicalDataList = filterNonEmptyClinicalData(sampleClinicalDataList);
@@ -30,10 +26,6 @@ public static List<ClinicalData> fetchClinicalDataForXyPlot(
         if (patientClinicalDataList.isEmpty()) {
             combinedClinicalDataList = sampleClinicalDataList;
         } else {
-            // fetch samples for the given study view filter.
-            // we need this to construct the complete patient to sample map. 
-            List<Sample> samples = studyViewColumnarService.getFilteredSamples(studyViewFilter);
-
             combinedClinicalDataList = Stream.concat(
                 sampleClinicalDataList.stream(),
                 convertPatientClinicalDataToSampleClinicalData(patientClinicalDataList, samples).stream()