Add isUnfiltered condition to cacheable clickhouse methods (#11120)

* add singleStudyUnfiltered condition to cacheable clickhouse methods * add condition for density and violin plot data methods * change singleStudyUnfiltered to just unfiltered --------- Co-authored-by: Bryan Lai <[email protected]>
cBioPortal · Oct 28, 2024 · d4fece4 · d4fece4
1 parent 6d87467
commit d4fece4
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Showing 9 changed files with 48 additions and 31 deletions.
diff --git a/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java b/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java
@@ -2,11 +2,12 @@
 
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.DensityPlotData;
+import org.cbioportal.web.parameter.StudyViewFilter;
 import org.cbioportal.web.util.DensityPlotParameters;
 
 import java.math.BigDecimal;
 import java.util.List;
 
 public interface ClinicalDataDensityPlotService {
-    DensityPlotData getDensityPlotData(List<ClinicalData> filteredClinicalData, DensityPlotParameters densityPlotParameters);
+    DensityPlotData getDensityPlotData(List<ClinicalData> filteredClinicalData, DensityPlotParameters densityPlotParameters, StudyViewFilter studyViewFilter);
 }
diff --git a/src/main/java/org/cbioportal/service/ViolinPlotService.java b/src/main/java/org/cbioportal/service/ViolinPlotService.java
@@ -3,6 +3,7 @@
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalViolinPlotData;
 import org.cbioportal.model.Sample;
+import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.math.BigDecimal;
 import java.util.List;
@@ -15,6 +16,7 @@ ClinicalViolinPlotData getClinicalViolinPlotData(
         BigDecimal axisEnd,
         BigDecimal numCurvePoints,
         Boolean useLogScale,
-        BigDecimal sigmaMultiplier
+        BigDecimal sigmaMultiplier,
+        StudyViewFilter studyViewFilter
     );
 }
diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java
@@ -8,6 +8,7 @@
 import org.cbioportal.model.DensityPlotData;
 import org.cbioportal.service.ClinicalDataDensityPlotService;
 import org.cbioportal.web.columnar.StudyViewColumnStoreController;
+import org.cbioportal.web.parameter.StudyViewFilter;
 import org.cbioportal.web.util.DensityPlotParameters;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
@@ -25,10 +26,10 @@ public class ClinicalDataDensityPlotServiceImpl implements ClinicalDataDensityPl
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
-    public DensityPlotData getDensityPlotData(List<ClinicalData> sampleClinicalData, DensityPlotParameters densityPlotParameters) {
+    public DensityPlotData getDensityPlotData(List<ClinicalData> sampleClinicalData, DensityPlotParameters densityPlotParameters, StudyViewFilter studyViewFilter) {
         DensityPlotData result = new DensityPlotData();
         result.setBins(new ArrayList<>());
 

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -51,11 +51,10 @@ public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository, Alt
         this.treatmentCountReportService = treatmentCountReportService;
         this.customDataFilterUtil = customDataFilterUtil;
     }
-
-    // should  condition = "@cacheEnabledConfig.getEnabledClickhouse() && #singleStudyUnfiltered" 
+
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter) {
@@ -65,7 +64,7 @@ public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter) {
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException {
@@ -74,7 +73,7 @@ public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilt
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilter studyViewFilter) {
@@ -83,7 +82,7 @@ public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilter st
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
@@ -92,7 +91,7 @@ public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter s
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
@@ -101,7 +100,7 @@ public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyVie
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
@@ -110,7 +109,7 @@ public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewF
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<GenomicDataBinFilter> genomicDataBinFilters) {
@@ -119,7 +118,7 @@ public List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter study
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataBinFilter> genericAssayDataBinFilters) {
@@ -132,7 +131,7 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter)
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException {
@@ -141,7 +140,7 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter stu
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
@@ -150,7 +149,7 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
@@ -169,7 +168,7 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
@@ -181,7 +180,7 @@ public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFi
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
@@ -190,7 +189,7 @@ public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
@@ -199,7 +198,7 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter,
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
@@ -208,7 +207,7 @@ public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter stu
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataFilter> genericAssayDataFilters) {
@@ -217,7 +216,7 @@ public List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilter
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
@@ -238,7 +237,7 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilte
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     @Override
     public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {

diff --git a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java
@@ -5,6 +5,7 @@
 import org.apache.commons.math3.stat.descriptive.rank.Percentile;
 import org.cbioportal.model.*;
 import org.cbioportal.service.ViolinPlotService;
+import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
@@ -20,7 +21,7 @@ public class ViolinPlotServiceImpl implements ViolinPlotService {
 
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
-        condition = "@cacheEnabledConfig.getEnabledClickhouse()"
+        condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfiltered(#studyViewFilter)"
     )
     public ClinicalViolinPlotData getClinicalViolinPlotData(
         List<ClinicalData> sampleClinicalDataForViolinPlot,
@@ -29,7 +30,8 @@ public ClinicalViolinPlotData getClinicalViolinPlotData(
         BigDecimal axisEnd,
         BigDecimal numCurvePoints,
         Boolean useLogScale,
-        BigDecimal sigmaMultiplier
+        BigDecimal sigmaMultiplier,
+        StudyViewFilter studyViewFilter
     ) {
         ClinicalViolinPlotData result = new ClinicalViolinPlotData();
         result.setAxisStart(Double.POSITIVE_INFINITY);

diff --git a/src/main/java/org/cbioportal/web/StudyViewController.java b/src/main/java/org/cbioportal/web/StudyViewController.java
@@ -862,7 +862,8 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(
             axisEnd,
             numCurvePoints,
             useLogScale,
-            sigmaMultiplier
+            sigmaMultiplier,
+            interceptedStudyViewFilter
         );
 
         return new ResponseEntity<>(result, HttpStatus.OK);

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -309,7 +309,7 @@ public ResponseEntity<DensityPlotData> fetchClinicalDataDensityPlot(
             .build();
 
         List<ClinicalData> sampleClinicalDataList = studyViewColumnarService.getSampleClinicalData(interceptedStudyViewFilter, xyAttributeId);
-        DensityPlotData result = clinicalDataDensityPlotService.getDensityPlotData(sampleClinicalDataList, densityPlotParameters);
+        DensityPlotData result = clinicalDataDensityPlotService.getDensityPlotData(sampleClinicalDataList, densityPlotParameters, interceptedStudyViewFilter);
 
         return new ResponseEntity<>(result, HttpStatus.OK);
     }
@@ -378,7 +378,8 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(
             axisEnd,
             numCurvePoints,
             useLogScale,
-            sigmaMultiplier
+            sigmaMultiplier,
+            interceptedStudyViewFilter
         );
 
         return new ResponseEntity<>(result, HttpStatus.OK);

diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java
@@ -200,8 +200,16 @@ public List<ClinicalDataCountItem> getClinicalDataCountsFromCustomData(Collectio
     }
 
     public boolean isSingleStudyUnfiltered(StudyViewFilter filter) {
+        return isSingleStudy(filter) && isUnfiltered(filter);
+    }
+
+    public boolean isSingleStudy(StudyViewFilter filter) {
+        return filter.getStudyIds() != null &&
+            filter.getStudyIds().size() == 1;
+    }
+
+    public boolean isUnfiltered(StudyViewFilter filter) {
         return filter.getStudyIds() != null &&
-            filter.getStudyIds().size() == 1 &&
             (filter.getClinicalDataFilters() == null || filter.getClinicalDataFilters().isEmpty()) &&
             (filter.getGeneFilters() == null || filter.getGeneFilters().isEmpty()) &&
             (filter.getSampleTreatmentFilters() == null || filter.getSampleTreatmentFilters().getFilters().isEmpty()) &&

diff --git a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java b/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java
@@ -4,6 +4,7 @@
 import org.cbioportal.model.ClinicalViolinPlotData;
 import org.cbioportal.model.ClinicalViolinPlotRowData;
 import org.cbioportal.model.Sample;
+import org.cbioportal.web.parameter.StudyViewFilter;
 import org.junit.Assert;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -77,7 +78,8 @@ public void getClinicalViolinPlotData() throws Exception {
             new BigDecimal(1),
             new BigDecimal(NUM_CURVE_POINTS),
             false,
-            new BigDecimal(1)
+            new BigDecimal(1),
+            new StudyViewFilter()
         );