Merge branch 'release-3.x.x' into TASK-6219

opencb · Nov 8, 2024 · 026635a · 026635a
2 parents ced9545 + feedb60
commit 026635a
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Showing 9 changed files with 358 additions and 230 deletions.
diff --git a/.../main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java b/.../main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java
@@ -239,8 +239,8 @@ public void checkCanAssignOrSeePermissions(String organizationId, long studyId,
 
     @Override
     public void checkCanCreateUpdateDeleteVariableSets(String organizationId, long studyId, String userId) throws CatalogException {
-        if (!isAtLeastOrganizationOwnerOrAdmin(organizationId, userId)) {
-            throw CatalogAuthorizationException.notOrganizationOwnerOrAdmin("create, update or delete variable sets.");
+        if (!isAtLeastStudyAdministrator(organizationId, studyId, userId)) {
+            throw CatalogAuthorizationException.notStudyAdmin("create, update or delete variable sets.");
         }
     }
 

diff --git a/...catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/AnnotationMongoDBAdaptor.java b/...catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/AnnotationMongoDBAdaptor.java
@@ -70,11 +70,23 @@ public abstract class AnnotationMongoDBAdaptor<T> extends CatalogMongoDBAdaptor
 
     protected abstract MongoDBCollection getCollection();
 
-    abstract OpenCGAResult<T> transactionalUpdate(ClientSession clientSession, T entry, ObjectMap parameters,
+    OpenCGAResult<T> transactionalUpdate(ClientSession clientSession, T entry, ObjectMap parameters,
                                                   List<VariableSet> variableSetList, QueryOptions queryOptions)
+            throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException {
+        return transactionalUpdate(clientSession, entry, parameters, variableSetList, queryOptions, true);
+    }
+
+    abstract OpenCGAResult<T> transactionalUpdate(ClientSession clientSession, T entry, ObjectMap parameters,
+                                                  List<VariableSet> variableSetList, QueryOptions queryOptions, boolean incrementVersion)
             throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException;
 
-    abstract OpenCGAResult<T> transactionalUpdate(ClientSession clientSession, long studyUid, Bson query, UpdateDocument updateDocument)
+    OpenCGAResult<T> transactionalUpdate(ClientSession clientSession, long studyUid, Bson query, UpdateDocument updateDocument)
+            throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException {
+        return transactionalUpdate(clientSession, studyUid, query, updateDocument, true);
+    }
+
+    abstract OpenCGAResult<T> transactionalUpdate(ClientSession clientSession, long studyUid, Bson query, UpdateDocument updateDocument,
+                                         boolean incrementVersion)
             throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException;
 
     public enum AnnotationSetParams implements QueryParam {

diff --git a/...g/src/main/java/org/opencb/opencga/catalog/db/mongodb/ClinicalAnalysisMongoDBAdaptor.java b/...g/src/main/java/org/opencb/opencga/catalog/db/mongodb/ClinicalAnalysisMongoDBAdaptor.java
@@ -355,20 +355,21 @@ OpenCGAResult transactionalUpdate(ClientSession clientSession, ClinicalAnalysis
 
     @Override
     OpenCGAResult<ClinicalAnalysis> transactionalUpdate(ClientSession clientSession, ClinicalAnalysis entry, ObjectMap parameters,
-                                                        List<VariableSet> variableSetList, QueryOptions queryOptions)
+                                                        List<VariableSet> variableSetList, QueryOptions queryOptions,
+                                                        boolean incrementVersion)
             throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException {
         throw new NotImplementedException("Please call to the other transactionalUpdate method passing the ClinicalAudit list");
     }
 
     @Override
     OpenCGAResult<ClinicalAnalysis> transactionalUpdate(ClientSession clientSession, long studyUid, Bson query,
-                                                        UpdateDocument updateDocument)
+                                                        UpdateDocument updateDocument, boolean incrementVersion)
             throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException {
         long tmpStartTime = startQuery();
 
         Document updateOperation = updateDocument.toFinalUpdateDocument();
         if (!updateOperation.isEmpty()) {
-            return versionedMongoDBAdaptor.update(clientSession, query, entryList -> {
+            SnapshotVersionedMongoDBAdaptor.FunctionWithException<ClinicalAnalysis> updateClinicalReferences = (clinicalList) -> {
                 logger.debug("Update clinical analysis. Query: {}, Update: {}", query.toBsonDocument(), updateDocument);
                 DataResult<?> update = clinicalCollection.update(clientSession, query, updateOperation, null);
 
@@ -385,7 +386,12 @@ OpenCGAResult<ClinicalAnalysis> transactionalUpdate(ClientSession clientSession,
 
                 logger.debug("{} clinical analyses successfully updated", update.getNumUpdated());
                 return endWrite(tmpStartTime, update.getNumMatches(), update.getNumUpdated(), Collections.emptyList());
-            }, null, null);
+            };
+            if (incrementVersion) {
+                return versionedMongoDBAdaptor.update(clientSession, query, null, updateClinicalReferences, null, null);
+            } else {
+                return versionedMongoDBAdaptor.updateWithoutVersionIncrement(clientSession, query, null, updateClinicalReferences);
+            }
         } else {
             throw new CatalogDBException("Nothing to update");
         }

diff --git a/...cga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/CohortMongoDBAdaptor.java b/...cga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/CohortMongoDBAdaptor.java
@@ -286,7 +286,7 @@ public OpenCGAResult update(Query query, ObjectMap parameters, List<VariableSet>
 
     @Override
     OpenCGAResult<Cohort> transactionalUpdate(ClientSession clientSession, Cohort cohort, ObjectMap parameters,
-                                              List<VariableSet> variableSetList, QueryOptions queryOptions)
+                                              List<VariableSet> variableSetList, QueryOptions queryOptions, boolean incrementVersion)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         long tmpStartTime = startQuery();
         Query tmpQuery = new Query()
@@ -341,7 +341,8 @@ OpenCGAResult<Cohort> transactionalUpdate(ClientSession clientSession, Cohort co
     }
 
     @Override
-    OpenCGAResult<Cohort> transactionalUpdate(ClientSession clientSession, long studyUid, Bson query, UpdateDocument updateDocument)
+    OpenCGAResult<Cohort> transactionalUpdate(ClientSession clientSession, long studyUid, Bson query, UpdateDocument updateDocument,
+                                              boolean incrementVersion)
             throws CatalogParameterException, CatalogDBException, CatalogAuthorizationException {
         long tmpStartTime = startQuery();