The goal of virtuoso is to provide an easy interface to Virtuoso RDF database from R.
Installation
You can install the development version of virtuoso from GitHub with:
remotes::install_github("cboettig/virtuoso")Getting Started
For Mac users, virtuoso package includes a utility
function to install and configure a local Virtuoso Open Source instance
using Homebrew. Otherwise, simply install the Virtuoso Open Source
edition for your operating system.
vos_install()
#> Virtuoso is already installed.We can now start our Virtuoso server from R:
vos_start()
#> PROCESS 'virtuoso-t', running, pid 352405.
#> Server is now starting up, this may take a few seconds...
#> latest log entry: 22:02:55 Server online at 1111 (pid 352405)Once the server is running, we can connect to the database.
con <- vos_connect()Our connection is now live, and accepts SPARQL queries directly.
DBI::dbGetQuery(con, "SPARQL SELECT * WHERE { ?s ?p ?o } LIMIT 4")
#> s
#> 1 http://www.openlinksw.com/virtrdf-data-formats#default-iid
#> 2 http://www.openlinksw.com/virtrdf-data-formats#default-iid-nullable
#> 3 http://www.openlinksw.com/virtrdf-data-formats#default-iid-nonblank
#> 4 http://www.openlinksw.com/virtrdf-data-formats#default-iid-nonblank-nullable
#> p o
#> 1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.openlinksw.com/schemas/virtrdf#QuadMapFormat
#> 2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.openlinksw.com/schemas/virtrdf#QuadMapFormat
#> 3 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.openlinksw.com/schemas/virtrdf#QuadMapFormat
#> 4 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.openlinksw.com/schemas/virtrdf#QuadMapFormatDSL
virtuoso also provides wrappers around some common
queries to make it easier to work with Virtuoso and RDF.
The bulk loader can be used to quickly import existing sets of triples.
example <- system.file("extdata", "person.nq", package = "virtuoso")
vos_import(con, example)Can also read in compressed formats as well. Remember to set the pattern match appropriately. This is convenient because N-Quads compress particularly well, often by a factor of 20 (or rather, can be particularly large when uncompressed, owing to the repeated property and subject URIs).
ex <- system.file("extdata", "library.nq.gz", package = "virtuoso")
vos_import(con, ex)vos_import invisibly returns a table of the loaded
files, with error message and loading times. If a file cannot be
imported, an error message is returned:
bad_file <- system.file("extdata", "bad_quads.nq", package = "virtuoso")
vos_import(con, bad_file)
#> Error: Error importing: bad_quads.nq 37000 SP029: NQuads RDF loader, line 2: Undefined namespace prefix at ITIS:1000000We can now query the imported data using SPARQL.
vos_query(con,
"SELECT ?p ?o
WHERE { ?s ?p ?o .
?s a <http://schema.org/Person>
}")
#> p o
#> 1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://schema.org/Person
#> 2 http://schema.org/jobTitle Professor
#> 3 http://schema.org/name Jane Doe
#> 4 http://schema.org/telephone (425) 123-4567
#> 5 http://schema.org/url http://www.janedoe.com
vos_query(con,
"SELECT ?p ?o
WHERE { ?s ?p ?o .
?s a <http://example.org/vocab#Chapter>
}")
#> p o
#> 1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://example.org/vocab#Chapter
#> 2 http://purl.org/dc/elements/1.1/description An introductory chapter on The Republic.
#> 3 http://purl.org/dc/elements/1.1/title The IntroductionServer controls
We can control any virtuoso server started with
vos_start() using a series of helper commands.
vos_status()
#> latest log entry: 22:02:56 PL LOG: No more files to load. Loader has finished,
#> [1] "sleeping"Advanced usage note: vos_start() invisibly returns a
processx object which we can pass to other server control
functions, or access the embedded processx control methods
directly. The virtuoso package also caches this object in
an environment so that it can be accessed directly without having to
keep track of an object in the global environment. Use
vos_process() to return the processx object.
For example:
library(ps)
p <- vos_process()
ps_is_running(p)
#> [1] TRUE
ps_cpu_times(p)
#> user system children_user children_system
#> 1.82 0.54 0.00 0.00
ps_suspend(p)
#> NULL
ps_resume(p)
#> NULL