Consistently use transactions to update database

For any action which is multi-step (requires updating more than 1 DB
key), use transaction to make update atomic.

Also pack big chunks of updates (importing packages for importing and
mirror updates) into single transaction to improve aptly performance and
get some isolation.

Note that still layers up (Collections) provide some level of isolation,
so this is going to shine with the future PRs to remove collection
locks.

Spin-off of #459

deb/publish.go

@@ -914,21 +914,27 @@ func (collection *PublishedRepoCollection) CheckDuplicate(repo *PublishedRepo) *
 }
 
 // Update stores updated information about repo in DB
-func (collection *PublishedRepoCollection) Update(repo *PublishedRepo) (err error) {
-	err = collection.db.Put(repo.Key(), repo.Encode())
+func (collection *PublishedRepoCollection) Update(repo *PublishedRepo) error {
+	transaction, err := collection.db.OpenTransaction()
 	if err != nil {
-		return
+		return err
+	}
+	defer transaction.Discard()
+
+	err = transaction.Put(repo.Key(), repo.Encode())
+	if err != nil {
+		return err
 	}
 
 	if repo.SourceKind == SourceLocalRepo {
 		for component, item := range repo.sourceItems {
-			err = collection.db.Put(repo.RefKey(component), item.packageRefs.Encode())
+			err = transaction.Put(repo.RefKey(component), item.packageRefs.Encode())
 			if err != nil {
-				return
+				return err
 			}
 		}
 	}
-	return
+	return transaction.Commit()
 }
 
 // LoadComplete loads additional information for remote repo
@@ -1170,6 +1176,13 @@ func (collection *PublishedRepoCollection) Remove(publishedStorageProvider aptly
 	storage, prefix, distribution string, collectionFactory *CollectionFactory, progress aptly.Progress,
 	force, skipCleanup bool) error {
 
+	transaction, err := collection.db.OpenTransaction()
+	if err != nil {
+		return err
+	}
+	defer transaction.Discard()
+
+	// TODO: load via transaction
 	collection.loadList()
 
 	repo, err := collection.ByStoragePrefixDistribution(storage, prefix, distribution)
@@ -1221,17 +1234,17 @@ func (collection *PublishedRepoCollection) Remove(publishedStorageProvider aptly
 		}
 	}
 
-	err = collection.db.Delete(repo.Key())
+	err = transaction.Delete(repo.Key())
 	if err != nil {
 		return err
 	}
 
 	for _, component := range repo.Components() {
-		err = collection.db.Delete(repo.RefKey(component))
+		err = transaction.Delete(repo.RefKey(component))
 		if err != nil {
 			return err
 		}
 	}
 
-	return nil
+	return transaction.Commit()
 }