Introduction: Virtuoso Installation and Configuration

Carl Boettiger

2024-11-27

Virtuoso is a high-performance “universal server” that can act as both a relational database (supporting standard SQL queries) and an RDF triplestore, (supporting SPARQL queries).
Virtuoso supports communication over the standard ODBC interface, and so R users can potentially connect to Virtuoso merely by installing the server and using the odbc R package. However, installation can present a few gotchas to users unfamiliar with Virtuoso. This package seeks to streamline the process of installing, managing, and querying a Virtuoso server. While the package can be also be used merely to provide a standard DBI connection to an RDBS, e.g. as a dplyr back-end, Virtuoso’s popularity and performance is particularly notable with respect to RDF data and SPARQL queries, so most examples focus on those use cases.

Installation

The virtuoso package provides installation helpers for both Mac OSX and Windows users through the function vos_install(). At the time of writing, the Mac OS X installer uses Homebrew to install the Virtuoso Open Source server (similar to the hugo installer in RStudio’s blogdown). On Windows, vos_install() downloads and executes the Windows self-extracting archive (.exe file), which will open a standard installation dialog in interactive mode, or be run automatically if not run in an interactive session. No automated installer is provided for Linux systems; Linux users are encouraged to simply install the appropriate binaries for their distribution (e.g. apt-get install -y virtuoso-opensource on Debian/Ubuntu systems).

Configuration

Virtuoso Open Source configuration is controlled by a virtouso.ini file, which sets, among other things, which directories can be accessed for tasks such as bulk import, as well as performance tweaks such as available memory. Unfortunately, the Virtuoso server process (virtuoso-t application) cannot start without a path to an appropriate config file, and the installers (e.g. on both Windows and Linux) frequently install an example virtuoso.ini to a location which can be hard to find and for which users do not have permission to edit directly. Moreover, the file format is not always intuitive to edit. The virtuoso package thus helps locate this file and provides a helper function, vos_configure(), to create and modify this configuration file. Because reasonable defaults are also provided by this function, users should usually not need to call this function manually. vos_configure() is called automatically from vos_start() if the path to a virtuoso.ini file is not passed to vos_start().

In addition to configuring Virtuoso’s settings through a virtuoso.ini file, the other common barrier is setting up the driver for the ODBC connection. Some installers (Mac, Linux) do not automatically add the appropriate driver to an active odbcinst.ini file with a predictable Driver Server Name, which we need to know to initiate the ODBC connection. An internal helper function handles identifying drivers and establishing the appropriate odcinst.ini automatically when necessary.

Server management

Lastly, Virtuoso Open Source is often run as a system service, starting when the operating system starts. This is often undesirable, as the casual laptop user does not want the service running all the time, and can be difficult to control for users unfamiliar with managing such background services on their operating systems. Instead of this behavior, the virtuoso package provides an explicit interface to control the external server. The server only starts when created by vos_start(), and ends automatically when the R process ends, or can be killed, paused, or resumed at any time from R (e.g. via vos_kill()). Helper utilities can also query the status and logs of the server from R. As with most database servers, data persists to disk, at an appropriate location for the OS determined by rappdirs package, and a helper utility, vos_delete_db() can remove this persistent storage location.

Users can also connect directly to any existing (local or remote) Virtuoso instance by passing the appropriate information to vos_connect(), which can be convenient for queries.

Note that he Virtuoso back-end provided by the R package rdflib can also connect to any Virtuoso server created by the virtuoso R package, though queries loading and queries through the redland libraries used by rdflib will generally be slower than direct calls over ODBC via the virtuoso package functions, often dramatically so for large triplestores.