Add a background migration to rename `uploads` in the uploads table

db/post_migrate/20170717150329_enqueue_migrate_system_uploads_to_new_folder.rb

+class EnqueueMigrateSystemUploadsToNewFolder < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  OLD_FOLDER = 'uploads/system/'
+  NEW_FOLDER = 'uploads/-/system/'
+
+  disable_ddl_transaction!
+
+  def up
+    BackgroundMigrationWorker.perform_async('MigrateSystemUploadsToNewFolder',
+                                            [OLD_FOLDER, NEW_FOLDER])
+  end
+
+  def down
+    BackgroundMigrationWorker.perform_async('MigrateSystemUploadsToNewFolder',
+                                            [NEW_FOLDER, OLD_FOLDER])
+  end
+end

db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
-ActiveRecord::Schema.define(version: 20170717111152) do
+ActiveRecord::Schema.define(version: 20170717150329) do
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"

lib/gitlab/background_migration/migrate_system_uploads_to_new_folder.rb

+module Gitlab
+  module BackgroundMigration
+    class MigrateSystemUploadsToNewFolder
+      include Gitlab::Database::MigrationHelpers
+      attr_reader :old_folder, :new_folder
+
+      def perform(old_folder, new_folder)
+        @old_folder = old_folder
+        @new_folder = new_folder
+
+        replace_sql = replace_sql(uploads[:path], old_folder, new_folder)
+
+        while remaining_rows > 0
+          sql = "UPDATE uploads "\
+                "SET path = #{replace_sql} "\
+                "WHERE uploads.id IN "\
+                "  (SELECT uploads.id FROM uploads "\
+                "  WHERE #{affected_uploads.to_sql} LIMIT 1000)"
+          connection.execute(sql)
+        end
+      end
+
+      def uploads
+        Arel::Table.new('uploads')
+      end
+
+      def remaining_rows
+        remaining_result = connection.exec_query("SELECT count(id) FROM uploads WHERE #{affected_uploads.to_sql}")
+        remaining = remaining_result.first['count'].to_i
+        logger.info "#{remaining} uploads remaining"
+        remaining
+      end
+
+      def affected_uploads
+        uploads[:path].matches("#{old_folder}%")
+      end
+
+      def connection
+        ActiveRecord::Base.connection
+      end
+
+      def logger
+        Sidekiq.logger || Rails.logger || Logger.new(STDOUT)
+      end
+    end
+  end
+end

spec/lib/gitlab/background_migration/migrate_system_uploads_to_new_folder_spec.rb

+require 'spec_helper'
+
+describe Gitlab::BackgroundMigration::MigrateSystemUploadsToNewFolder do
+  let(:migration) { described_class.new }
+
+  before do
+    allow(migration).to receive(:logger).and_return(Logger.new(nil))
+  end
+
+  describe '#perform' do
+    it 'renames the path of system-uploads', truncate: true do
+      upload = create(:upload, model: create(:empty_project), path: 'uploads/system/project/avatar.jpg')
+
+      migration.perform('uploads/system/', 'uploads/-/system/')
+
+      expect(upload.reload.path).to eq('uploads/-/system/project/avatar.jpg')
+    end
+  end
+end