make xy plot data cacheable

cBioPortal · Dec 12, 2024 · 6109444 · 6109444
1 parent fa1e4f3
commit 6109444
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Showing 4 changed files with 37 additions and 17 deletions.
diff --git 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
@@ -28,13 +28,14 @@
 import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
-import org.cbioportal.web.parameter.SampleIdentifier;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.cbioportal.web.columnar.util.CustomDataFilterUtil;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
+import static org.cbioportal.web.columnar.util.ClinicalDataXyPlotUtil.combineClinicalDataForXyPlot;
+
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -276,6 +277,33 @@ 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
@@ -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
@@ -12,15 +12,13 @@
 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 +28,6 @@ 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()