# Running Virtuoso ## Tags * type: documentation * status: unclear ## Description We run instances of Virtuoso for our graph databases. Virtuoso is a remarkable software and running some really large databases, including Uniprot => https://github.com/openlink/virtuoso-opensource => https://www.uniprot.org/sparql/ On Penguin2 virtuoso is running by default as a shepherd servive, see => ./shepherd.gmi ``` guix environment --ad-hoc virtuoso-ose -- virtuoso-t -f ``` => https://git.genenetwork.org/efraim/shepherd-services/src/branch/master/shepherd/init.d/virtuoso.scm penguin2:/home/shepherd/shepherd-services/shepherd/init.d/virtuoso.scm The database is initialized from 'penguin2:/export/virtuoso/var/lib/virtuoso/db/virtuoso.ini' ### Running a new instance For testing we want to run a temporary instance. Let's start from the virtuoso.ini file: ``` mkdir -p ~/services/virtuoso cd services/virtuoso cp /export/virtuoso/var/lib/virtuoso/db/virtuoso.ini . ``` and edit it to change paths and ports - use non-priviliged ports(!). A full diff is below. Start the server in a screen or tmux (it may ask for creating ./db): ``` penguin2:~/services/virtuoso$ ~/.config/guix/current/bin/guix environment --ad-hoc virtuoso-ose glibc-locales penguin2:~/services/virtuoso$ /gnu/store/9aqd4jmkafhkdm095hnmxpxzws3ym3wd-virtuoso-ose-7.2.5/bin/virtuoso-t +foreground +configfile virtuoso.ini 03:34:50 HTTP/WebDAV server online at 28890 03:34:50 Server online at 21111 (pid 57078) ``` Now the server should respond to ``` curl localhost:28890/sparql ``` and the admin interface on ``` curl localhost:28890/conductor ``` To use the service from your remote machine use ssh tunnels: ``` ssh -L 28890:127.0.0.1:28890 -f -N myname@penguin2.genenetwork.org ``` and surf to http://localhost:28890/conductor. A good time to change the default password (dba:dba)! ### Uploading data with CURL To upload RDF I use rapper to validate the data. First delete the existing graph with something like ``` curl -v --digest --user dba:password --verbose --url -G http://localhost:28890/sparql-graph-crud-auth --data-urlencode graph=https://BioHackrXiv.org/graph -X DELETE ``` Next update the graph with ``` curl -v -X PUT --digest -u dba:password -H Content-Type:text/turtle -T test/data/biohackrxiv.ttl -G http://localhost:28890/sparql-graph-crud-auth --data-urlencode graph=https://BioHackrXiv.org/graph ``` Where BioHackrXiv is the name of the graph (in this example). A python version can be found in => https://github.com/pubseq/bh20-seq-resource/blob/master/scripts/update_virtuoso/check_for_updates.py ### Virtuoso.ini What changed in $HOME/services/virtuoso/virtuoso.ini ``` +DatabaseFile = $HOME/services/virtuoso/db/virtuoso.db +ErrorLogFile = $HOME/services/virtuoso/db/virtuoso.log +LockFile = $HOME/services/virtuoso/db/virtuoso.lck +TransactionFile = $HOME/services/virtuoso/db/virtuoso.trx +xa_persistent_file = $HOME/services/virtuoso/db/virtuoso.pxa +DatabaseFile = $HOME/services/virtuoso/db/virtuoso-temp.db +TransactionFile = $HOME/services/virtuoso/db/virtuoso-temp.trx -ServerPort = 1111 +ServerPort = 21111 +NumberOfBuffers = 340000 +MaxDirtyBuffers = 250000 +ServerPort = 28890 +ServerRoot = $HOME/services/virtuoso/vsp ```