Setting up Virtuoso

OpenLink Virtuoso triplestore is available on DockerHub.

Run it

Be careful when changing the DBA_PASSWORD for tenforce/virtuoso. This doesn't work every time, so you might need to use the default dba password.

docker run --rm --name d2s-virtuoso \

--network d2s-core_network \

-p 8890:8890 -p 1111:1111 \

-e DBA_PASSWORD=dba \

-e SPARQL_UPDATE=true \

-e DEFAULT_GRAPH=https://w3id.org/d2s/graph \

-v /data/virtuoso:/data \

-d umids/d2s-virtuoso

Access at http://localhost:8890/ and SPARQL endpoint at http://localhost:8890/sparql.

Admin login: dba / dba

Shared in /data/virtuoso

Use the Search Index

Example working on DBpedia and Bio2RDF:

SELECT ?foundUri ?foundLabel WHERE {?foundUri <http://www.w3.org/2000/01/rdf-schema#label> ?foundLabel . ?foundLabel bif:contains '$TEXT_TO_SEARCH' . } LIMIT 200

Enable Virtuoso full text index following this documentation.

Clear Virtuoso triplestore

docker exec -it d2s-virtuoso isql-v -U dba -P dba exec="RDF_GLOBAL_RESET ();"

RDF bulk load

This command should work to load all .nq files in the workspace/virtuoso directory, but it seems to have issues:

docker exec -it d2s-virtuoso isql-v -U dba -P dba exec="ld_dir('/usr/local/virtuoso-opensource/var/lib/virtuoso/db', '*.nq', 'http://test/'); rdf_loader_run();"

This command is used by the CWL workflow, but fails when run manually:

docker exec -i d2s-virtuoso bash -c "/load.sh" "/usr/local/virtuoso-opensource/var/lib/virtuoso/db" "rdf_output.nq" "https://w3id.org/d2s/graph/default" "rdf_output_vload.log" "dba"

For some reason the args are not passed to the script 🚧

Dump graphs

See the official documentation for dumping and loading graphs.

Dump one graph

See Virtuoso documentation to dump a specific graph as Turtle (.ttl)

First create the dump_one_graph procedure according to the documentation.

See example to dump the Bio2RDF ClinicalTrials Graph from Virtuoso:

docker exec -i d2s-virtuoso isql-v -U dba -P dba exec="dump_one_graph ('http://bio2rdf.org/clinicaltrials_resource:bio2rdf.dataset.clinicaltrials.R3', '/usr/local/virtuoso-opensource/var/lib/virtuoso/db/dumps/clinicaltrials', 999999999999999);"

Dump all graphs

See Virtuoso documentation to dump all graphs as Nquads.

First create the dump_nquads procedure according to the documentation.

See example to dump a complete Virtuoso triplestore:

docker exec -i d2s-virtuoso isql-v -U dba -P dba exec="dump_nquads ('dumps', 1, 999999999999999, 1);"

Configuration

CORS can be enabled following this tutorial.