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cBioPortal · Jan 19, 2025 · 670ffff · 670ffff
1 parent 31c3842
commit 670ffff
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Showing 6 changed files with 103 additions and 32 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java b/src/main/java/org/cbioportal/persistence/cachemaputil/CacheMapBuilder.java
@@ -10,15 +10,18 @@
 import org.cbioportal.persistence.MolecularProfileRepository;
 import org.cbioportal.persistence.SampleListRepository;
 import org.cbioportal.persistence.StudyRepository;
+import org.cbioportal.service.impl.vs.VirtualStudyService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Stream;
 
 @Component
 public class CacheMapBuilder {
@@ -28,6 +31,11 @@ public class CacheMapBuilder {
     @Autowired
     private StudyRepository studyRepository;
 
+    @Autowired
+    private VirtualStudyService virtualStudyService;
+
+    @Value("${vs_mode:false}") Boolean vsMode;
+
     @Autowired
     private MolecularProfileRepository molecularProfileRepository;
 
@@ -65,13 +73,16 @@ public Map<String, SampleList> buildSampleListMap() {
     }
 
     public Map<String, CancerStudy> buildCancerStudyMap() {
-        Map<String, CancerStudy> cancerStudyMap = studyRepository.getAllStudies(
-            null,
-            "SUMMARY",
-            REPOSITORY_RESULT_LIMIT,
-            REPOSITORY_RESULT_OFFSET,
-            null,
-            "ASC").stream()
+        Map<String, CancerStudy> cancerStudyMap = Stream.concat(
+                studyRepository.getAllStudies(
+                null,
+                "SUMMARY",
+                REPOSITORY_RESULT_LIMIT,
+                REPOSITORY_RESULT_OFFSET,
+                null,
+                "ASC").stream(),
+                vsMode ? virtualStudyService.findVirtualStudies(null).stream() : Stream.empty()
+                )
             .collect(Collectors.toMap(CancerStudy::getCancerStudyIdentifier, Function.identity()));
         LOG.debug("  cancer study map size: " + cancerStudyMap.size());
         return cancerStudyMap;

diff --git a/src/main/java/org/cbioportal/service/impl/vs/VSAwareServicesConfiguration.java b/src/main/java/org/cbioportal/service/impl/vs/VSAwareServicesConfiguration.java
@@ -1,5 +1,6 @@
 package org.cbioportal.service.impl.vs;
 
+import org.cbioportal.service.CancerTypeService;
 import org.cbioportal.service.ReadPermissionService;
 import org.cbioportal.service.StudyService;
 import org.cbioportal.service.util.SessionServiceRequestHandler;
@@ -36,7 +37,7 @@ public Executor asyncExecutor() {
 
     @Primary
     @Bean
-    public StudyService studyService(StudyService studyService, Executor asyncExecutor) {
-        return new VSAwareStudyServiceImpl(studyService, sessionServiceRequestHandler, readPermissionService, asyncExecutor);
+    public StudyService studyService(StudyService studyService, VirtualStudyService virtualStudyService, Executor asyncExecutor) {
+        return new VSAwareStudyServiceImpl(studyService, virtualStudyService, 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
@@ -3,8 +3,10 @@
 import org.cbioportal.model.CancerStudy;
 import org.cbioportal.model.CancerStudyTags;
 import org.cbioportal.model.meta.BaseMeta;
+import org.cbioportal.service.CancerTypeService;
 import org.cbioportal.service.ReadPermissionService;
 import org.cbioportal.service.StudyService;
+import org.cbioportal.service.exception.CancerTypeNotFoundException;
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.service.util.SessionServiceRequestHandler;
 import org.cbioportal.utils.security.AccessLevel;
@@ -25,14 +27,13 @@ public class VSAwareStudyServiceImpl implements StudyService {
 
     private final StudyService studyService;
 
-    private final SessionServiceRequestHandler sessionServiceRequestHandler;
-
     private final ReadPermissionService readPermissionService;
     private final Executor asyncExecutor;
+    private final VirtualStudyService virtualStudyService;
 
-    public VSAwareStudyServiceImpl(StudyService studyService, SessionServiceRequestHandler sessionServiceRequestHandler, ReadPermissionService readPermissionService, Executor asyncExecutor) {
+    public VSAwareStudyServiceImpl(StudyService studyService, VirtualStudyService virtualStudyService, ReadPermissionService readPermissionService, Executor asyncExecutor) {
         this.studyService = studyService;
-        this.sessionServiceRequestHandler = sessionServiceRequestHandler;
+        this.virtualStudyService = virtualStudyService;
         this.readPermissionService = readPermissionService;
         this.asyncExecutor = asyncExecutor;
     }
@@ -59,27 +60,20 @@ public List<CancerStudy> getAllStudies(String keyword, String projection, Intege
         readPermissionService.setReadPermission(result, authentication);
         return result;
     }
-
+    //TODO these should not fail the whole request if one of them fails
     @Async
     private CompletableFuture<List<CancerStudy>> getVirtualStudiesAsync(String keyword) {
-        return CompletableFuture.supplyAsync(() -> sessionServiceRequestHandler.getVirtualStudiesAccessibleToUser("*").stream()
-                .map(VSAwareStudyServiceImpl::toCancerStudy).filter(cs -> shouldSelect(cs, keyword)).toList(), asyncExecutor);
+        return CompletableFuture.supplyAsync(() -> virtualStudyService.findVirtualStudies(keyword), asyncExecutor);
+                //TODO return empty list if the request fails
+                //.exceptionally(e -> List.of());
     }
 
     @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();
-        cs.setCancerStudyIdentifier(vs.getId());
-        cs.setName(vsd.getName());
-        cs.setDescription(vsd.getDescription());
-        cs.setPmid(vsd.getPmid());
-        return cs;
-    }
+
 
     private static Comparator<CancerStudy> buildComparator(String sortBy, String direction) {
         Function<CancerStudy, Comparable> getValue;
@@ -98,10 +92,7 @@ private static Comparator<CancerStudy> buildComparator(String sortBy, String dir
         throw new IllegalArgumentException("Invalid direction value: " + direction);
     }
 
-    private static boolean shouldSelect(CancerStudy cs, String keyword) {
-        //TODO improve the search. The keyword can be also sent to mongo to search for virtual studies
-        return cs.getName().toLowerCase().contains(keyword.toLowerCase());
-    }
+
 
     @Override
     public BaseMeta getMetaStudies(String keyword) {
@@ -119,7 +110,7 @@ public CancerStudy getStudy(String studyId) throws StudyNotFoundException {
 
     @Async
     private CompletableFuture<Optional<CancerStudy>> getVirtualStudyAsync(String studyId) {
-        return CompletableFuture.supplyAsync(() -> Optional.ofNullable(sessionServiceRequestHandler.getVirtualStudyById(studyId)).map(VSAwareStudyServiceImpl::toCancerStudy), asyncExecutor);
+        return CompletableFuture.supplyAsync(() -> virtualStudyService.findVirtualStudy(studyId), asyncExecutor);
     }
 
     @Async
@@ -153,8 +144,10 @@ private static <T> CompletableFuture<Optional<T>> firstPresent(
     public List<CancerStudy> fetchStudies(List<String> studyIds, String projection) {
         List<CancerStudy> materialisedStudies = studyService.fetchStudies(studyIds, projection);
         List<String> notFoundStudyIds = materialisedStudies.stream().map(CancerStudy::getCancerStudyIdentifier).filter(studyId -> !studyIds.contains(studyId)).toList();
-        //TODO implement using completable futures. It must be better for IO bound operations
-        List<CancerStudy> virtualStudies = notFoundStudyIds.parallelStream().map(sessionServiceRequestHandler::getVirtualStudyById).map(VSAwareStudyServiceImpl::toCancerStudy).toList();
+        //TODO implement using completable futures. It must be better for IO bound operations. Fetch all instead of one by one
+        List<CancerStudy> virtualStudies = notFoundStudyIds.parallelStream().map(virtualStudyService::findVirtualStudy)
+            .flatMap(Optional::stream)
+            .toList();
         return Stream.concat(materialisedStudies.stream(), virtualStudies.stream()).toList();
     }
 

diff --git a/src/main/java/org/cbioportal/service/impl/vs/VirtualStudyService.java b/src/main/java/org/cbioportal/service/impl/vs/VirtualStudyService.java
@@ -0,0 +1,63 @@
+package org.cbioportal.service.impl.vs;
+
+import org.cbioportal.model.CancerStudy;
+import org.cbioportal.service.CancerTypeService;
+import org.cbioportal.service.exception.CancerTypeNotFoundException;
+import org.cbioportal.service.util.SessionServiceRequestHandler;
+import org.cbioportal.web.parameter.VirtualStudy;
+import org.cbioportal.web.parameter.VirtualStudyData;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class VirtualStudyService {
+
+    private final CancerTypeService cancerTypeService;
+    private final SessionServiceRequestHandler sessionServiceRequestHandler;
+
+    public VirtualStudyService(SessionServiceRequestHandler sessionServiceRequestHandler, CancerTypeService cancerTypeService) {
+        this.sessionServiceRequestHandler = sessionServiceRequestHandler;
+        this.cancerTypeService = cancerTypeService;
+    }
+
+    public List<CancerStudy> findVirtualStudies(String keyword) {
+        return sessionServiceRequestHandler.getVirtualStudiesAccessibleToUser("*").stream()
+            .map(this::toCancerStudy).filter(cs -> shouldSelect(cs, keyword)).toList();
+    }
+
+    public Optional<CancerStudy> findVirtualStudy(String id) {
+        return Optional.ofNullable(sessionServiceRequestHandler.getVirtualStudyById(id)).map(this::toCancerStudy);
+    }
+
+    private CancerStudy toCancerStudy(VirtualStudy vs) {
+        VirtualStudyData vsd = vs.getData();
+        CancerStudy cs = new CancerStudy();
+        cs.setCancerStudyIdentifier(vs.getId());
+        cs.setName(vsd.getName());
+        //TODO fetch mixed cancer type in the constructor once. To fail initialization if the type is not found
+        String typeOfCancerId = vsd.getTypeOfCancerId() == null ? "mixed" : vsd.getTypeOfCancerId();
+        try {
+            cs.setTypeOfCancer(cancerTypeService.getCancerType(typeOfCancerId));
+            cs.setTypeOfCancerId(typeOfCancerId);
+        } catch (CancerTypeNotFoundException e) {
+            throw new RuntimeException(e);
+        }
+        cs.setDescription(vsd.getDescription());
+        cs.setPmid(vsd.getPmid());
+        //TODO run filters on the dynamic virtual study
+        cs.setAllSampleCount(vsd.getStudies().stream().map(s -> s.getSamples().size()).reduce(0, Integer::sum));
+        //TODO we can implement this field for published virtual studies to predefine rights on groups even before the study is created
+        cs.setGroups("PUBLIC");
+        return cs;
+    }
+
+    private static boolean shouldSelect(CancerStudy cs, String keyword) {
+        //TODO improve the search. The keyword can be also sent to mongo to search for virtual studies
+        if (keyword == null) {
+            return true;
+        }
+        return cs.getName().toLowerCase().contains(keyword.toLowerCase());
+    }
+}
diff --git a/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java b/src/main/java/org/cbioportal/web/PublicVirtualStudiesController.java
@@ -93,6 +93,7 @@ public ResponseEntity<Void> unPublishVirtualStudy(
      * @param pmid  - if specified (not null) update PubMed ID of published virtual study
      */
     private void publishVirtualStudy(String id, String typeOfCancerId, String pmid) {
+        //TODO add to cahce map when vs_mode is true
         VirtualStudy virtualStudyDataToPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
         VirtualStudyData virtualStudyData = virtualStudyDataToPublish.getData();
         updateStudyMetadataFieldsIfSpecified(virtualStudyData, typeOfCancerId, pmid);
@@ -105,6 +106,7 @@ private void publishVirtualStudy(String id, String typeOfCancerId, String pmid)
      * @param id - id of public virtual study to un-publish
      */
     private void unPublishVirtualStudy(String id) {
+        //TODO remove from cahce map when vs_mode is true
         VirtualStudy virtualStudyToUnPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
         if (virtualStudyToUnPublish == null) {
             throw new NoSuchElementException("The virtual study with id=" + id + " has not been found in the public list.");

diff --git a/src/test/resources/seed_mini.sql b/src/test/resources/seed_mini.sql
@@ -81,6 +81,7 @@ INSERT INTO "type_of_cancer" ("TYPE_OF_CANCER_ID","NAME","DEDICATED_COLOR","SHOR
 INSERT INTO "type_of_cancer" ("TYPE_OF_CANCER_ID","NAME","DEDICATED_COLOR","SHORT_NAME","PARENT") VALUES ('blca','Bladder Urothelial Carcinoma','Yellow','Bladder','tissue');
 INSERT INTO "type_of_cancer" ("TYPE_OF_CANCER_ID","NAME","DEDICATED_COLOR","SHORT_NAME","PARENT") VALUES ('bpdcn','Blastic Plasmacytoid Dendritic Cell Neoplasm','LightSalmon','BPDCN','tissue');
 INSERT INTO "type_of_cancer" ("TYPE_OF_CANCER_ID","NAME","DEDICATED_COLOR","SHORT_NAME","PARENT") VALUES ('brca','Breast Invasive Carcinoma','HotPink','Breast','tissue');
+INSERT INTO "type_of_cancer" ("TYPE_OF_CANCER_ID","NAME","DEDICATED_COLOR","SHORT_NAME","PARENT") VALUES ('mixed','Mixed Cancer Types','Yellow','Mixed','tissue');
 
 -- reference_genome
 INSERT INTO `reference_genome` VALUES (1,'human','hg19','GRCh37',2897310462,'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips','2009-02-01');