More fixes

Author: forus

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, CancerTypeService cancerTypeService, Executor asyncExecutor) {
+        return new VSAwareStudyServiceImpl(studyService, sessionServiceRequestHandler, readPermissionService, cancerTypeService, asyncExecutor);
     }
 }

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;
@@ -29,11 +31,13 @@ public class VSAwareStudyServiceImpl implements StudyService {
 
     private final ReadPermissionService readPermissionService;
     private final Executor asyncExecutor;
+    private final CancerTypeService cancerTypeService;
 
-    public VSAwareStudyServiceImpl(StudyService studyService, SessionServiceRequestHandler sessionServiceRequestHandler, ReadPermissionService readPermissionService, Executor asyncExecutor) {
+    public VSAwareStudyServiceImpl(StudyService studyService, SessionServiceRequestHandler sessionServiceRequestHandler, ReadPermissionService readPermissionService, CancerTypeService cancerTypeService, Executor asyncExecutor) {
         this.studyService = studyService;
         this.sessionServiceRequestHandler = sessionServiceRequestHandler;
         this.readPermissionService = readPermissionService;
+        this.cancerTypeService = cancerTypeService;
         this.asyncExecutor = asyncExecutor;
     }
 
@@ -59,25 +63,34 @@ 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);
+                .map(this::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) {
+    private CancerStudy toCancerStudy(VirtualStudy vs) {
         VirtualStudyData vsd = vs.getData();
         CancerStudy cs = new CancerStudy();
         cs.setCancerStudyIdentifier(vs.getId());
         cs.setName(vsd.getName());
+        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 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;
     }
 
@@ -100,6 +113,9 @@ private static Comparator<CancerStudy> buildComparator(String sortBy, String dir
 
     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());
     }
 
@@ -119,7 +135,7 @@ 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(() -> Optional.ofNullable(sessionServiceRequestHandler.getVirtualStudyById(studyId)).map(this::toCancerStudy), asyncExecutor);
     }
 
     @Async
@@ -154,7 +170,7 @@ 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();
+        List<CancerStudy> virtualStudies = notFoundStudyIds.parallelStream().map(sessionServiceRequestHandler::getVirtualStudyById).map(this::toCancerStudy).toList();
         return Stream.concat(materialisedStudies.stream(), virtualStudies.stream()).toList();
     }
 

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',null,'Mixed',null);
 
 -- reference_genome
 INSERT INTO `reference_genome` VALUES (1,'human','hg19','GRCh37',2897310462,'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips','2009-02-01');