Merge pull request #2429 from opencb/TASK-6019

TASK-6019 - Note migration may raise errors

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/NoteMigration.java

@@ -3,7 +3,10 @@
 import com.mongodb.MongoNamespace;
 import com.mongodb.client.MongoCollection;
 import com.mongodb.client.model.Filters;
+import com.mongodb.client.model.RenameCollectionOptions;
 import com.mongodb.client.model.Updates;
+import com.mongodb.client.result.UpdateResult;
+import org.apache.commons.lang3.StringUtils;
 import org.bson.Document;
 import org.bson.conversions.Bson;
 import org.opencb.commons.datastore.mongodb.MongoDataStore;
@@ -18,6 +21,9 @@
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.models.notes.Note;
 
+import java.util.Collections;
+import java.util.List;
+
 @Migration(id = "migrate_notes", description = "Migrate notes #TASK-5836", version = "3.1.0",
         language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240315)
 public class NoteMigration extends MigrationTool {
@@ -35,28 +41,42 @@ protected void run() throws Exception {
                 Updates.set(NoteDBAdaptor.QueryParams.STUDY.key(), ""),
                 Updates.set(NoteDBAdaptor.QueryParams.VISIBILITY.key(), Note.Visibility.PRIVATE.name())
         );
-        collection.updateMany(query, update);
-        renameNoteCollection();
+        UpdateResult updateResult = collection.updateMany(query, update);
+        if (updateResult.getModifiedCount() == 0) {
+            // Check there are at least 2 organizations present
+            logger.info("Note data model could not be updated. Detected organizations are: {}", StringUtils.join(dbAdaptorFactory.getOrganizationIds(), ","));
+            if (dbAdaptorFactory.getOrganizationIds().size() == 2) {
+                logger.info("Nothing to migrate");
+                return;
+            } else {
+                throw new CatalogDBException("Notes could not be found to migrate.");
+            }
+        }
+        renameNoteCollection(Collections.singletonList(ParamConstants.ADMIN_ORGANIZATION));
 
         dbAdaptorFactory.close();
         dbAdaptorFactory = new MongoDBAdaptorFactory(configuration, ioManagerFactory);
         // We run it a second time because the first time it will only rename the "opencga" org as OpenCGA will not be able to know
         // which other organizations are present in the installation (trying to fetch the information from "note" instead of old "notes")
-        renameNoteCollection();
+        List<String> organizationIds = dbAdaptorFactory.getOrganizationIds();
+        organizationIds.remove(ParamConstants.ADMIN_ORGANIZATION);
+        renameNoteCollection(organizationIds);
 
         // Reload catalog manager to install missing indexes
         catalogManager = new CatalogManager(configuration);
         catalogManager.installIndexes(token);
     }
 
-    private void renameNoteCollection() throws CatalogDBException {
+    private void renameNoteCollection(List<String> organizationIds) throws CatalogDBException {
+        RenameCollectionOptions options = new RenameCollectionOptions().dropTarget(true);
         // Rename collection
-        for (String organizationId : dbAdaptorFactory.getOrganizationIds()) {
+        for (String organizationId : organizationIds) {
             String databaseName = dbAdaptorFactory.getMongoDataStore(organizationId).getDatabaseName();
+            logger.info("Renaming notes collection for organization '{}' -> Database: '{}'", organizationId, databaseName);
             MongoDataStore mongoDataStore = dbAdaptorFactory.getMongoDataStore(organizationId);
-            mongoDataStore.getDb().getCollection("notes").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION));
-            mongoDataStore.getDb().getCollection("notes_archive").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION));
-            mongoDataStore.getDb().getCollection("notes_deleted").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.DELETED_NOTE_COLLECTION));
+            mongoDataStore.getDb().getCollection("notes").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION), options);
+            mongoDataStore.getDb().getCollection("notes_archive").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION), options);
+            mongoDataStore.getDb().getCollection("notes_deleted").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.DELETED_NOTE_COLLECTION), options);
         }
     }