Merge branch 'demo-rfc80-poc' into rfc80/clinical-data-counts-refactor

cBioPortal · Nov 6, 2024 · fcba20d · fcba20d
2 parents 9c534e8 + 9782432
commit fcba20d
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Showing 30 changed files with 407 additions and 125 deletions.
diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java
@@ -1,6 +1,8 @@
 package org.cbioportal.model;
 
-public class ClinicalViolinPlotBoxData {
+import java.io.Serializable;
+
+public class ClinicalViolinPlotBoxData implements Serializable {
     private double whiskerLower;
     private double whiskerUpper;
     private double median;

diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java
@@ -1,8 +1,9 @@
 package org.cbioportal.model;
 
+import java.io.Serializable;
 import java.util.List;
 
-public class ClinicalViolinPlotData {
+public class ClinicalViolinPlotData implements Serializable {
     private List<ClinicalViolinPlotRowData> rows;
     private Double axisStart;
     private Double axisEnd;

diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java
@@ -1,6 +1,8 @@
 package org.cbioportal.model;
 
-public class ClinicalViolinPlotIndividualPoint {
+import java.io.Serializable;
+
+public class ClinicalViolinPlotIndividualPoint implements Serializable {
     private String sampleId;
     private String studyId;
     private double value;

diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java
@@ -1,8 +1,9 @@
 package org.cbioportal.model;
 
+import java.io.Serializable;
 import java.util.List;
 
-public class ClinicalViolinPlotRowData {
+public class ClinicalViolinPlotRowData implements Serializable {
     private String category;
     private Integer numSamples;
     private List<Double> curveData;

diff --git a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java b/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java
@@ -16,8 +16,11 @@ public class CacheEnabledConfig {
 
     @Value("${persistence.cache_type:no-cache}")
     private String cacheType;
+    @Value("${persistence.cache_type_clickhouse:no-cache}")
+    private String cacheTypeClickhouse;
 
     private boolean enabled;
+    private boolean enabledClickhouse;
 
     public static final String EHCACHE_DISK = "ehcache-disk";
     public static final String EHCACHE_HEAP = "ehcache-heap";
@@ -30,6 +33,8 @@ public class CacheEnabledConfig {
     public void init() {
         this.enabled = enableCache(cacheType);
         LOG.info("Cache is enabled: " + this.enabled);
+        this.enabledClickhouse = enableCache(cacheTypeClickhouse);
+        LOG.info("Cache is enabled for clickhouse: " + this.enabledClickhouse);
     }
 
     public static boolean enableCache(String cacheType) {
@@ -53,4 +58,16 @@ public boolean isEnabled() {
         return enabled;
     }
 
+    public String getEnabledClickhouse() {
+        if (enabledClickhouse) {
+            return "true";
+        } else {
+            return "false";
+        }
+    }
+
+    public boolean isEnabledClickhouse() {
+        return enabledClickhouse;
+    }
+
 }
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -29,6 +29,8 @@
 public interface StudyViewRepository {
     List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterContext);
 
+    List<String> getFilteredStudyIds(StudyViewFilterContext studyViewFilterContext);
+
     List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);
 
     List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);

diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java b/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java
@@ -57,6 +57,8 @@ public class SpringManagedCacheMapUtil implements CacheMapUtil {
 
     @Value("${persistence.cache_type:no-cache}")
     private String cacheType;
+    @Value("${persistence.cache_type_clickhouse:no-cache}")
+    private String cacheTypeClickhouse;
 
     @Value("${cache.cache-map-utils.spring-managed}")
     private boolean springManagedCacheMapUtils;
@@ -67,7 +69,7 @@ public class SpringManagedCacheMapUtil implements CacheMapUtil {
     @PostConstruct
     public void init() {
         // Make sure the user does not have a conflicting configuration. Explode if there is.
-        if (cacheType.equals("no-cache") && springManagedCacheMapUtils) {
+        if (cacheType.equals("no-cache") && cacheTypeClickhouse.equals("no-cache") && springManagedCacheMapUtils) {
             throw new RuntimeException("cache.cache-map-utils.spring-managed property is set to 'true' but the portal is not " +
                 "configured with a cache-implementation (persistence.cache_type property is 'no-cache'). Please set to 'false'" +
                 " or configure the cache.");

diff --git a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java b/src/main/java/org/cbioportal/persistence/config/RedisConfig.java
@@ -3,8 +3,8 @@
 import org.cbioportal.persistence.util.CustomKeyGenerator;
 import org.cbioportal.persistence.util.CustomRedisCachingProvider;
 import org.cbioportal.persistence.util.LoggingCacheErrorHandler;
-import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
 import org.springframework.cache.CacheManager;
 import org.springframework.cache.annotation.CachingConfigurerSupport;
 import org.springframework.cache.annotation.EnableCaching;
@@ -18,7 +18,9 @@
 
 @Configuration
 @EnableCaching
-@ConditionalOnProperty(name = "persistence.cache_type", havingValue = {"redis"})
+@ConditionalOnExpression(
+    "#{environment['persistence.cache_type'] == 'redis' or environment['persistence.cache_type_clickhouse'] == 'redis'}"
+)
 public class RedisConfig extends CachingConfigurerSupport {
 
     @Value("${redis.name:cbioportal}")

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -30,6 +30,8 @@
 
 public interface StudyViewMapper {
     List<Sample> getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
+
+    List<String> getFilteredStudyIds(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
     List<GenomicDataCount> getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -55,7 +55,12 @@ public StudyViewMyBatisRepository(StudyViewMapper mapper) {
     public List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterContext) {
         return mapper.getFilteredSamples(createStudyViewFilterHelper(studyViewFilterContext));
     }
-
+
+    @Override
+    public List<String> getFilteredStudyIds(StudyViewFilterContext studyViewFilterContext) {
+        return mapper.getFilteredStudyIds(createStudyViewFilterHelper(studyViewFilterContext));
+    }
+
     @Override
     public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
         return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext),

diff --git a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java b/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java
@@ -64,7 +64,7 @@ public class CustomKeyGenerator implements KeyGenerator {
     private static final Logger LOG = LoggerFactory.getLogger(CustomKeyGenerator.class);
 
     public Object generate(Object target, Method method, Object... params) {
-        if (!cacheEnabledConfig.isEnabled()) {
+        if (!cacheEnabledConfig.isEnabled() && !cacheEnabledConfig.isEnabledClickhouse()) {
             return "";
         }
         String key = target.getClass().getSimpleName() + CACHE_KEY_PARAM_DELIMITER

diff --git a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java b/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java
@@ -3,9 +3,9 @@
 import static org.cbioportal.persistence.util.CustomRedisCache.DELIMITER;
 
 
-import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.redisson.api.RedissonClient;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;
 import org.springframework.stereotype.Component;
@@ -14,7 +14,9 @@
 import java.util.stream.Collectors;
 
 @Component
-@ConditionalOnProperty(name = "persistence.cache_type", havingValue = "redis")
+@ConditionalOnExpression(
+    "#{environment['persistence.cache_type'] == 'redis' or environment['persistence.cache_type_clickhouse'] == 'redis'}"
+)
 public class RedisCacheUtils implements CacheUtils {
 
     @Autowired

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/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -391,7 +391,7 @@ private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
     }
 
     private Map<String, MutSig> getMutSigs(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException {
-        var distinctStudyIds = new HashSet<>(studyViewFilterContext.studyViewFilter().getStudyIds()).stream().toList();
+        var distinctStudyIds = studyViewRepository.getFilteredStudyIds(studyViewFilterContext);
         Map<String, MutSig> mutSigs = new HashMap<>();
         if (distinctStudyIds.size() == 1) {
             var studyId = distinctStudyIds.getFirst();
@@ -409,7 +409,7 @@ private Map<String, MutSig> getMutSigs(StudyViewFilterContext studyViewFilterCon
     }
 
     private Map<Pair<String, Integer>, Gistic> getGisticMap(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException {
-        var distinctStudyIds = new HashSet<>(studyViewFilterContext.studyViewFilter().getStudyIds()).stream().toList();
+        var distinctStudyIds = studyViewRepository.getFilteredStudyIds(studyViewFilterContext);
         Map<Pair<String, Integer>, Gistic> gisticMap = new HashMap<>(); 
         if (distinctStudyIds.size() == 1) {
             var studyId = distinctStudyIds.getFirst();

diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java
@@ -8,7 +8,9 @@
 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;
 
 import java.math.BigDecimal;
@@ -18,15 +20,21 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
+
 @Service
 public class ClinicalDataDensityPlotServiceImpl implements ClinicalDataDensityPlotService {
+
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver",
+        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<>());
 
         Map<String, List<ClinicalData>> clinicalDataGroupedBySampleId = sampleClinicalData.stream().
-            collect(Collectors.groupingBy(ClinicalData::getSampleId));
+            collect(Collectors.groupingBy(c -> c.getStudyId() + "_" + c.getSampleId()));
 
         List<ClinicalData> extractedXYClinicalData = clinicalDataGroupedBySampleId.entrySet().stream()
             .filter(entry -> entry.getValue().size() == 2 &&

diff --git a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java
@@ -7,6 +7,7 @@
 import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;
 import org.springframework.security.access.AccessDeniedException;
@@ -19,7 +20,9 @@
 import java.util.stream.Collectors;
 
 @Service
-@ConditionalOnProperty(name = "persistence.cache_type", havingValue = {"redis"})
+@ConditionalOnExpression(
+    "#{environment['persistence.cache_type'] == 'redis' or environment['persistence.cache_type_clickhouse'] == 'redis'}"
+)
 public class RedisCacheStatisticsServiceImpl implements CacheStatisticsService {
 
     @Autowired