Working with Database Storage Backends in `rdflib`
In rdflib: Tools to Manipulate and Query Semantic Data

By default, rdflib stores triples in memory, which can be read in from and written out to files on disk using a variety of serializations (rdfxml, json-ld, ntriples, nquads or turtle). This is analgous to reading in a data.frame object from a csv, tsv, or other text-delimited file, which requires the full data object to be read into memory before a user can manipulate it. This approach runs into limitations with very large datasets, which may exceed the memory available. Just as R packages such as dplyr offer the ability to perform manipulations with very large data through a connection to a database backend such as SQLite, MySQL or PostgreSQL, rdflib can rely on these and other databases to provide a disk-based backend.

Installation

Unfortunately, at this time, support for these storage devices is not included in the prebuild Mac and Windows binaries of the redland R package. Users wanting to take advantage of disk-based storage must instead build and install the redland R package from source; and in some cases, also build the redland C libraries from source. This package provides a Dockerfile containing a portable recipe for building the library with support for the 5 main backend storage devices: SQLite, MySQL, PostgreSQL, Virtuoso, and Berkeley DB. This vignette documents the installation and use of these devices.

Also see the official documentation for the redland C library discussing all supported storage devices.

Benchmarks

Here we show examples of reading in a modest set of 190,000 triples from an nquads file and executing a simple SPARQL query using each the five backends supported by rdflib. First we load the libraries and prepare an example file by triple-ifying 10,000 rows of the flights data.frame:

library(rdflib)
library(nycflights13)

example <- flights[1e4,]

system.time(
write_nquads(example, "example.nq", prefix = "flights")
)
#>    user  system elapsed 
#>   0.009   0.001   0.008

system.time(
write_nquads(flights, "flights.nq", prefix = "flights")
)
#>    user  system elapsed 
#>  15.107   0.474  15.632

In Memory

Because the dataset is small enough to easily fit in memory, the default in-memory option is an obvious choice with excellent performance. Note that this option will not be possible with larger triplestores (e.g. with millions or more triples). Our testing has found that even on machines with 100GB+ of RAM, the redland in-memory backend is not able to take advantage of that additional memory and disk-based backends are required.

triplestore <- rdf()

system.time(
  read_nquads("example.nq", rdf = triplestore) # smaller set
)
#>    user  system elapsed 
#>   0.002   0.000   0.002

query <- 
  'SELECT  ?carrier ?flight ?origin ?dep_delay
WHERE {
?flight <flights:carrier>  ?carrier .
?flight <flights:dep_delay>  ?dep_delay .
?flight <flights:origin> ?origin
}'

system.time(
df <- rdf_query(triplestore, query)
)
#>    user  system elapsed 
#>   0.011   0.008   0.019

rdf_free(triplestore)

BDB

The Berkeley DB is a simple key-value store

It is the most mature and primary persistent store and suitable for large models, tested in the 2-3 million range.

Berkeley DB is a simple disk-based storage option. Install both the redland libraries and the berkeley-db (e.g. bd-dev on Debian/Ubuntu) libraries, and then install redland from source. BDB is relatively fast for data too large for memory.

triplestore <- rdf(storage="BDB", new_db = TRUE)
system.time(
  read_nquads("flights.nq", rdf = triplestore)
)
#>    user  system elapsed 
#>  55.985  15.686  71.787

system.time(
df <- rdf_query(triplestore, query)
)
#>    user  system elapsed 
#>  15.001   0.216  15.222

rdf_free(triplestore)
## Becuase BDB is just a hash table, redland needs three separate files:
unlink("rdflib-po2s.db")
unlink("rdflib-so2p.db")
unlink("rdflib-sp2o.db")

Virtuoso

Unlike the other backends which use general purpose relational databases or key-value stores, Virtuoso dedicated to RDF-based data. Virtuoso is a popular open source database for RDF with a rich set of built-in interfaces and features, but we can also interact with it directly through the redland bindings just like we do any other backend in rdflib. Virtuoso setup may be slightly more involved for individuals unfamiliar with it, but will probably provide the best performance in the case of very large triplestores. The example below shows a new database setup, but rdflib can also connect to any existing Virtuoso database.

triplestore <- rdf(storage = "virtuoso", 
                   user = "dba", 
                   password = "dba", 
                   dsn = "Local Virtuoso"
                   )

system.time(
  read_nquads("flights.nq", rdf = triplestore)
)
#>     user   system  elapsed 
#>  111.500   84.856 3336.717

system.time(
df <- rdf_query(triplestore, query)
)
#>    user  system elapsed 
#>  17.899   9.056 133.143
df <- rdf_query(triplestore, "SELECT ?s ?p ?o WHERE{ ?s ?p ?o }")
#> Warning: 1391187 parsing failures.
#>     row col expected     actual         file
#> 1338850   o a double _:r1011167 literal data
#> 1338851   o a double _:r1011168 literal data
#> 1338852   o a double _:r1011169 literal data
#> 1338853   o a double _:r1011170 literal data
#> 1338854   o a double _:r1012106 literal data
#> ....... ... ........ .......... ............
#> See problems(...) for more details.
df
#> # A tibble: 6,398,744 x 3
#>    s          p                o
#>    <chr>      <chr>        <dbl>
#>  1 flights:1  flights:year  2013
#>  2 flights:2  flights:year  2013
#>  3 flights:3  flights:year  2013
#>  4 flights:4  flights:year  2013
#>  5 flights:5  flights:year  2013
#>  6 flights:6  flights:year  2013
#>  7 flights:7  flights:year  2013
#>  8 flights:8  flights:year  2013
#>  9 flights:9  flights:year  2013
#> 10 flights:10 flights:year  2013
#> # … with 6,398,734 more rows

rdf_free(triplestore)

Or on remote virtuoso:

triplestore <- rdf(storage = "virtuoso", 
                   user = "dba", 
                   password = "dba", 
                   host = "virtuoso:1111"
                   )

system.time(
  read_nquads("flights.nq", rdf = triplestore)
)
#>       user     system    elapsed 
#> 129710.695   2036.842 149941.651

POSTGRES

Postgres and MySQL are ubiquitious relational databases. This backend requires the redland binaries are built from source with this support enabled, which is not the case for pre-built Mac or Linux binaries.

triplestore <- rdf(storage = "postgres", 
                   host = "postgres", 
                   user = "postgres", 
                   password = "rdflib", 
                   new_db = TRUE)
#> Warning in rdf_storage(storage, world, host, port, user, password,
#> database, : postgres driver not found. Falling back on in-memory storage
system.time(
  read_nquads("flights.nq", rdf = triplestore)
)
#>    user  system elapsed 
#>  31.803  20.715  52.586

system.time(
df <- rdf_query(triplestore, query)
)
#>    user  system elapsed 
#>   5.449   0.032   5.483

rdf_free(triplestore)

MySQL

triplestore <- rdf(storage = "mysql", 
                   host = "mariadb", 
                   user = "root", 
                   password = "rdflib", 
                   database = "mysql",
                   new_db = TRUE
                  )
#> Warning in rdf_storage(storage, world, host, port, user, password,
#> database, : mysql driver not found. Falling back on in-memory storage
  read_nquads("flights.nq", rdf = triplestore)
#> Total of 1996496 triples, stored in hashes
#> -------------------------------
#>  
#>  (preview supressed for performance)

system.time(df <- rdf_query(triplestore, query))
#>    user  system elapsed 
#>   5.510   0.004   5.515

rdf_free(triplestore)

SQLite

SQLite is relatively easy to set up, but appears to have rather poor overall performance. Requires SQLite development libraries installed (should work 'out-of-the-box' with Mac binaries for redland package).

triplestore <- rdf(storage="sqlite", new_db = TRUE, name="rdflib.sqlite")
#> Warning in rdf_storage(storage, world, host, port, user, password,
#> database, : sqlite driver not found. Falling back on in-memory storage

system.time(
  read_nquads("flights.nq", rdf = triplestore)
)
#>    user  system elapsed 
#>  31.607  20.219  51.857

system.time(
df <- rdf_query(triplestore, query)
)
#>    user  system elapsed 
#>   5.559   0.028   5.588

rdf_free(triplestore)

Building redland with full backend support

Getting full support for the above backend databases through the redland R package is not trivial. The redland R package provides bindings to the redland libraries. Unfortunately, commonly available binary versions of those libraries, such as librdf0-dev on Debian, redland on Mac OSX brew, and the statically linked versions for Mac and Windows shipping in the R package, do not build those libraries with the optional support for all backends. (NOTE: it is the C library itself which must be built from source with these options, not just the R package source). Consequently, users must build librdf from the original sources, https://github.com/dajobe/librdf with all backend linking libraries available, and then also build the redland R package from source, to be able to access all of these backends. On a Debian or Ubuntu system this looks like the following:

apt-get update && apt-get -yq install \
libxml2-dev \
libcurl4-openssl-dev \
libssl-dev \
git \
automake \
libtool \
gtk-doc-tools \
bison \
flex \
libgmp-dev  \
libmhash-dev \
libgcrypt20-dev \
libpcre3-dev \
libv8-dev \
libjq-dev \
libpq-dev \
libdb-dev \
libsqlite3-dev \
libmariadbclient-dev \
librdf-storage-virtuoso \
virtuoso-server \
unixodbc-dev

Now we can build raptor (parsers), rasqal (sparql queries) and rdflib from source:

git clone git://github.com/dajobe/raptor.git && \
cd raptor && \
./autogen.sh && \
make && \
make install && \
cd .. && \
git clone git://github.com/dajobe/rasqal.git && \
cd rasqal && \
./autogen.sh && \
make && \
make install && \
cd .. && \
git clone git://github.com/dajobe/librdf.git && \
cd librdf && \
./autogen.sh && \
make && \
make install

A See the Dockerfile in inst/docker for an example of this, or simply use the Rocker-based image ropensci/rdflib.

Testing

rdflib uses Circle-CI to test database backends using docker-compose. docker-compose pulls down dedicated docker containers for postgres and mariadb, along with the ropensci/rdflib container, which includes a version of redland compiled with support for all five major backend storage systems. See the Dockerfile in inst/docker and associated [docker-compose.yml]((https://github.com/ropensci/rdflib/tree/master/docker-compose.yml) used in testing for an example of this configuration. You can also pull the Docker image ropensci/rdflib from Docker Hub for testing with all these libraries installed.

The badge below (also on the package README) indicates that these dedicated tests are passing.