Re-apply caching to all study view service methods (#11091)

cBioPortal · Oct 18, 2024 · eee49e0 · eee49e0
1 parent 38a398d
commit eee49e0
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Showing 4 changed files with 96 additions and 6 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java
@@ -9,6 +9,7 @@
 import org.cbioportal.service.ClinicalDataDensityPlotService;
 import org.cbioportal.web.columnar.StudyViewColumnStoreController;
 import org.cbioportal.web.util.DensityPlotParameters;
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
 import java.math.BigDecimal;
@@ -18,8 +19,14 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
+
 @Service
 public class ClinicalDataDensityPlotServiceImpl implements ClinicalDataDensityPlotService {
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public DensityPlotData getDensityPlotData(List<ClinicalData> sampleClinicalData, DensityPlotParameters densityPlotParameters) {
         DensityPlotData result = new DensityPlotData();

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -52,43 +52,75 @@ public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository, Alt
         this.customDataFilterUtil = customDataFilterUtil;
     }
 
-    @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
+    // should  condition = "@cacheEnabledConfig.getEnabled() && #singleStudyUnfiltered" 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter) {
 
         return studyViewRepository.getFilteredSamples(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException {
         return alterationCountService.getMutatedGenes(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilter studyViewFilter) {
         return studyViewRepository.getMolecularProfileSampleCounts(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
         return studyViewRepository.getClinicalEventTypeCounts(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
         return treatmentCountReportService.getPatientTreatmentReport(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
         return treatmentCountReportService.getSampleTreatmentReport(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<ClinicalDataCountItem> getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List<GenomicDataBinFilter> genomicDataBinFilters) {
         return generateDataCountItemsFromDataCounts(studyViewRepository.getGenomicDataBinCounts(createContext(studyViewFilter), genomicDataBinFilters));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<ClinicalDataCountItem> getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataBinFilter> genericAssayDataBinFilters) {
         return generateDataCountItemsFromDataCounts(studyViewRepository.getGenericAssayDataBinCounts(createContext(studyViewFilter), genericAssayDataBinFilters));
@@ -98,16 +130,28 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter)
         return alterationCountService.getCnaGenes(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException {
         return alterationCountService.getStructuralVariantGenes(createContext(studyViewFilter));
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
         return studyViewRepository.getClinicalAttributeDatatypeMap();
     }
-
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
         StudyViewFilterContext studyViewFilterContext = createContext(studyViewFilter);
@@ -123,34 +167,58 @@ public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyVi
         );
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
         // the study view merges case lists by type across studies
         // type is determined by the suffix of case list name (after study name)
         var caseListDataCountsPerStudy = studyViewRepository.getCaseListDataCountsPerStudy(createContext(studyViewFilter));
         return mergeCaseListCounts(caseListDataCountsPerStudy);
     }
-
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
         return studyViewRepository.getPatientClinicalData(createContext(studyViewFilter), attributeIds);
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
         return studyViewRepository.getSampleClinicalData(createContext(studyViewFilter), attributeIds);
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         return studyViewRepository.getCNACounts(createContext(studyViewFilter), genomicDataFilters);
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataFilter> genericAssayDataFilters) {
         return studyViewRepository.getGenericAssayDataCounts(createContext(studyViewFilter), genericAssayDataFilters);
     }
-
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();
@@ -168,11 +236,16 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilte
         return genomicDataCountItemList;
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     @Override
     public List<GenomicDataCountItem> getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         return studyViewRepository.getMutationCountsByType(createContext(studyViewFilter), genomicDataFilters);
     }
 
+
     private StudyViewFilterContext createContext(StudyViewFilter studyViewFilter) {
         List<CustomSampleIdentifier> customSampleIdentifiers = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
         return new StudyViewFilterContext(studyViewFilter, customSampleIdentifiers);

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.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
 
 import java.math.BigDecimal;
@@ -16,7 +17,11 @@ public class ViolinPlotServiceImpl implements ViolinPlotService {
     // If a row has less than this many points, do not compute a
     //  violin, because it doesn't make sense.
     static final int SHOW_ONLY_POINTS_THRESHOLD = 7;
-
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     public ClinicalViolinPlotData getClinicalViolinPlotData(
         List<ClinicalData> sampleClinicalDataForViolinPlot,
         List<Sample> samplesForSampleCounts,

diff --git a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java b/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java
@@ -14,6 +14,7 @@
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.cbioportal.web.util.DataBinner;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Component;
 
 import java.util.*;
@@ -41,7 +42,11 @@ private List<ClinicalData> convertCountsToData(List<ClinicalDataCount> clinicalD
             .flatMap(Collection::stream)
             .toList();
     }
-
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        condition = "@cacheEnabledConfig.getEnabled()"
+    )
     public List<ClinicalDataBin> fetchClinicalDataBinCounts(
         DataBinMethod dataBinMethod,
         ClinicalDataBinCountFilter dataBinCountFilter,