Fix issues while testing the code

cBioPortal · Jan 17, 2025 · 31c3842 · 31c3842
1 parent e186354
commit 31c3842
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Showing 3 changed files with 51 additions and 12 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/vs/VSAwareServicesConfiguration.java b/src/main/java/org/cbioportal/service/impl/vs/VSAwareServicesConfiguration.java
@@ -8,6 +8,10 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+import org.springframework.security.concurrent.DelegatingSecurityContextExecutor;
+
+import java.util.concurrent.Executor;
 
 @Configuration
 @ConditionalOnProperty(name = "vs_mode", havingValue = "true")
@@ -19,9 +23,20 @@ public class VSAwareServicesConfiguration {
     @Autowired
     private ReadPermissionService readPermissionService;
 
+    @Bean
+    public Executor asyncExecutor() {
+        ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
+        executor.setCorePoolSize(10);
+        executor.setMaxPoolSize(20);
+        executor.setQueueCapacity(50);
+        executor.setThreadNamePrefix("AsyncThread-");
+        executor.initialize();
+        return new DelegatingSecurityContextExecutor(executor);
+    }
+
     @Primary
     @Bean
-    public StudyService studyService(StudyService studyService) {
-        return new VSAwareStudyServiceImpl(studyService, sessionServiceRequestHandler, readPermissionService);
+    public StudyService studyService(StudyService studyService, Executor asyncExecutor) {
+        return new VSAwareStudyServiceImpl(studyService, sessionServiceRequestHandler, readPermissionService, asyncExecutor);
     }
 }
diff --git a/src/main/java/org/cbioportal/service/impl/vs/VSAwareStudyServiceImpl.java b/src/main/java/org/cbioportal/service/impl/vs/VSAwareStudyServiceImpl.java
@@ -10,12 +10,14 @@
 import org.cbioportal.utils.security.AccessLevel;
 import org.cbioportal.web.parameter.VirtualStudy;
 import org.cbioportal.web.parameter.VirtualStudyData;
+import org.springframework.scheduling.annotation.Async;
 import org.springframework.security.core.Authentication;
 
 import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
 import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Executor;
 import java.util.function.Function;
 import java.util.stream.Stream;
 
@@ -26,18 +28,19 @@ public class VSAwareStudyServiceImpl implements StudyService {
     private final SessionServiceRequestHandler sessionServiceRequestHandler;
 
     private final ReadPermissionService readPermissionService;
+    private final Executor asyncExecutor;
 
-    public VSAwareStudyServiceImpl(StudyService studyService, SessionServiceRequestHandler sessionServiceRequestHandler, ReadPermissionService readPermissionService) {
+    public VSAwareStudyServiceImpl(StudyService studyService, SessionServiceRequestHandler sessionServiceRequestHandler, ReadPermissionService readPermissionService, Executor asyncExecutor) {
         this.studyService = studyService;
         this.sessionServiceRequestHandler = sessionServiceRequestHandler;
         this.readPermissionService = readPermissionService;
+        this.asyncExecutor = asyncExecutor;
     }
 
     @Override
     public List<CancerStudy> getAllStudies(String keyword, String projection, Integer pageSize, Integer pageNumber, String sortBy, String direction, Authentication authentication, AccessLevel accessLevel) {
-        CompletableFuture<List<CancerStudy>> materialisedStudies = CompletableFuture.supplyAsync(() -> studyService.getAllStudies(keyword, projection, null, null, null, null, authentication, accessLevel));
-        CompletableFuture<List<CancerStudy>> virtualStudies = CompletableFuture.supplyAsync(() ->  sessionServiceRequestHandler.getVirtualStudiesAccessibleToUser("*").stream()
-            .map(VSAwareStudyServiceImpl::toCancerStudy).filter(cs -> shouldSelect(cs, keyword)).toList());
+        CompletableFuture<List<CancerStudy>> materialisedStudies = getMaterialisedStudiesAsync(keyword, projection, authentication, accessLevel);
+        CompletableFuture<List<CancerStudy>> virtualStudies = getVirtualStudiesAsync(keyword);
 
         Stream<CancerStudy> resultStream = Stream.concat(
             materialisedStudies.join().stream(),
@@ -49,14 +52,25 @@ public List<CancerStudy> getAllStudies(String keyword, String projection, Intege
         }
 
         if (pageSize != null && pageNumber != null) {
-            resultStream = resultStream.skip((long) pageSize * (pageNumber - 1)).limit(pageSize);
+            resultStream = resultStream.skip((long) pageSize * pageNumber).limit(pageSize);
         }
 
         List<CancerStudy> result = resultStream.toList();
         readPermissionService.setReadPermission(result, authentication);
         return result;
     }
 
+    @Async
+    private CompletableFuture<List<CancerStudy>> getVirtualStudiesAsync(String keyword) {
+        return CompletableFuture.supplyAsync(() -> sessionServiceRequestHandler.getVirtualStudiesAccessibleToUser("*").stream()
+                .map(VSAwareStudyServiceImpl::toCancerStudy).filter(cs -> shouldSelect(cs, keyword)).toList(), asyncExecutor);
+    }
+
+    @Async
+    private CompletableFuture<List<CancerStudy>> getMaterialisedStudiesAsync(String keyword, String projection, Authentication authentication, AccessLevel accessLevel) {
+        return CompletableFuture.supplyAsync(() -> studyService.getAllStudies(keyword, projection, null, null, null, null, authentication, accessLevel), asyncExecutor);
+    }
+
     private static CancerStudy toCancerStudy(VirtualStudy vs) {
         VirtualStudyData vsd = vs.getData();
         CancerStudy cs = new CancerStudy();
@@ -98,15 +112,25 @@ public BaseMeta getMetaStudies(String keyword) {
 
     @Override
     public CancerStudy getStudy(String studyId) throws StudyNotFoundException {
-        CompletableFuture<Optional<CancerStudy>> materialisedStudy = CompletableFuture.supplyAsync(() -> {
+        CompletableFuture<Optional<CancerStudy>> materialisedStudy = getMaterialisedStudyAsync(studyId);
+        CompletableFuture<Optional<CancerStudy>> virtualStudy = getVirtualStudyAsync(studyId);
+        return firstPresent(materialisedStudy, virtualStudy).join().orElseThrow(() -> new StudyNotFoundException(studyId));
+    }
+
+    @Async
+    private CompletableFuture<Optional<CancerStudy>> getVirtualStudyAsync(String studyId) {
+        return CompletableFuture.supplyAsync(() -> Optional.ofNullable(sessionServiceRequestHandler.getVirtualStudyById(studyId)).map(VSAwareStudyServiceImpl::toCancerStudy), asyncExecutor);
+    }
+
+    @Async
+    private CompletableFuture<Optional<CancerStudy>> getMaterialisedStudyAsync(String studyId) {
+        return CompletableFuture.supplyAsync(() -> {
             try {
                 return Optional.of(studyService.getStudy(studyId));
             } catch (StudyNotFoundException e) {
                 return Optional.empty();
             }
-        });
-        CompletableFuture<Optional<CancerStudy>> virtualStudy = CompletableFuture.supplyAsync(() -> Optional.ofNullable(sessionServiceRequestHandler.getVirtualStudyById(studyId)).map(VSAwareStudyServiceImpl::toCancerStudy));
-        return firstPresent(materialisedStudy, virtualStudy).join().orElseThrow(() -> new StudyNotFoundException(studyId));
+        }, asyncExecutor);
     }
 
     private static <T> CompletableFuture<Optional<T>> firstPresent(

diff --git a/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java b/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java
@@ -47,7 +47,7 @@ public PublicVirtualStudiesController(
         @Value("${session.endpoint.publisher-api-key:}") String requiredPublisherApiKey,
         SessionServiceRequestHandler sessionServiceRequestHandler,
         CancerTypeService cancerTypeService,
-        @Value("vs_mode") Boolean vsMode
+        @Value("${vs_mode:false}") Boolean vsMode
     ) {
         this.requiredPublisherApiKey = requiredPublisherApiKey;
         this.sessionServiceRequestHandler = sessionServiceRequestHandler;