This page contains out-of-date information. If you are interested running a SPARQL endpoint with VIVO version 1.5 or 1.6, refer to the Setting up a VIVO SPARQL Endpoint page. |
This wiki page entitled How to install a Joseki SPARQL endpoint for VIVO was adapted from the text based HOWTO on the VIVO Sourceforge downloads section. It is meant to serve as a starting point for setting up your SPARQL endpoint for VIVO using the Joseki software that is part of the Jena project. The example details installing a Joseki SPARQL endpoint using the VIVO Virtual BOX virtual appliance. The most important part of the example comes from showing how to setup the Joskei config file called Joseki-config.ttl to hook up to your VIVO triple store. Also, this example instruction set assumes you are installing on Debian Linux or a Debian variant like Ubuntu. If you have VIVO running on another system you will have to follow the Joseki install instructions for your system and then use the sample Joseki-config.ttl provided. WARNING!- If you don't want anonymous updates via your spark-ly new SPARQL endpoint then please make sure you follow instructions for adding a filter in step 8 below. Comments on improving this page are very welcome. Good luck and good SPARQL-ing.
Note that the Apache Jena project is close to a 1.0 release of Fuseki – new 1.0 and 1.01 snapshots
Fuseki configuration for VIVO shared by NickV, 9/9/13:
# Licensed under the terms of http://www.apache.org/licenses/LICENSE-2.0
@prefix : <#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix jumble: <http://rootdev.net/vocab/jumble#> .
@prefix sdb: <http://jena.hpl.hp.com/2007/sdb#> .
[] rdf:type fuseki:Server ;
# Timeout - server-wide default: milliseconds.
# Format 1: "1000" -- 1 second timeout
# Format 2: "10000,60000" -- 10s timeout to first result, then 60s timeout to for rest of query.
# See java doc for ARQ.queryTimeout
ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "10000,60000" ] ;
fuseki:services (
<#service_VIVO_read_only>
) .
# SDB
[] ja:loadClass "net.rootdev.fusekisdbconnect.SDBConnect" .
jumble:SDBConnect rdfs:subClassOf ja:RDFDataset .
<#service_VIVO_read_only> rdf:type fuseki:Service ;
rdfs:label "TUe VIVO Service (R)" ;
fuseki:name "VIVO" ;
fuseki:serviceQuery "query" ;
fuseki:serviceQuery "sparql" ;
#fuseki:serviceUpdate "update" ;
#fuseki:serviceUpload "upload" ;
#fuseki:serviceReadWriteGraphStore "data" ;
# A separate read-only graph store endpoint:
#fuseki:serviceReadGraphStore "get" ;
fuseki:dataset <#ufvivo_dataset_read> ;
#fuseki:dataset <#VIVOStore> ;
.
<#ufvivo_dataset_read> rdf:type sdb:DatasetStore ;
sdb:store <#VIVOStore>
.
<#VIVOStore> rdf:type jumble:SDBConnect;
rdfs:label "TUE VIVO SDB Store";
sdb:layout "layout2";
jumble:defaultUnionGraph "true" ;
sdb:engine "InnoDB";
sdb:connection
[ rdf:type sdb:SDBConnection;
sdb:sdbHost "localhost";
sdb:sdbType "MySQL";
sdb:sdbName "vivo";
sdb:sdbUser "private";
sdb:sdbPassword "private";
sdb:driver "com.mysql.jdbc.Driver";
]
.
|
Download and set up a VIVO virtual appliance from:
http://sourceforge.net/projects/vivo/files/VIVO%20Virtual%20Appliances/ |
Note: all the shell commands are assuming you are on the console of the virtual appliance, but they should work on any Debian system. Virtual Machine Install Documentation is available at:
http://vivoweb.org/support/user-guide/installation
After installation and configuration, start the virtual appliance and login to the
command line interface. The username is vitro. The password is vitro123.
Change directories
vitro@vivo:/usr/local$ cd /usr/local |
Download Joseki from:
vitro@vivo:/usr/local$ sudo wget http://sourceforge.net/projects/joseki/files/Joseki-SPARQL/Joseki-3.4.2/joseki-3.4.2.zip/download |
Install unzip, needed to unpack the Joseki ZIP file
vitro@vivo:/usr/local$ sudo apt-get install unzip |
Unzip Joseki in usr/ocal
vitro@vivo:/usr/local$ sudo unzip joseki-3.4.2.zip |
Make the script in bin executable
vitro@vivo:/usr/local/Joseki-3.4.2$ cd Joseki-3.4.2 |
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo chmod u+x bin/*
See below for #Configuration for VIVO version 1.3.
Backup the config file
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo cp joseki-config.ttl joseki-config.default |
Make the new Joseki config file
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo touch joseki-config-vivo.ttl |
Edit the config file
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo nano joseki-config-vivo.ttl |
First, we declare some prefixes, then some basic information about this
file. Because the configuration file is RDF, order of the sections
does not matter to the server but it does help a human reading the
file. Copy and paste the following config file into the joseki-config.ttl:
COPY THE FOLLOWING TEXT INTO YOUR CONFIG
## --------------------------------------------------------------
# Title: VIVO Joseki example config
# Author(s): cpb@ufl.edu, drspeedo@ufl.edu
# ModDate: 20100805
# ShortDescR: This is an example joseki config to access vivo
# data using the joseki service.
# Warranty: Use at your own risk.
## --------------------------------------------------------------
# This file is written in N3 / Turtle
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix module: <http://joseki.org/2003/06/module#> .
@prefix joseki: <http://joseki.org/2005/06/configuration#> .
@prefix ql: <http://jena.hpl.hp.com/2003/07/query/> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
## --------------------------------------------------------------
## This file is written in N3 / Turtle
## It is an RDF graph - order of RDF triples does not matter
## to the machine but it does help people who need to edit this file.
## --------------------------------------------------------------
## Note: adding rdfs:label to blank nodes will cause Joseki
## to print that in log messages.
## --------------------------------------------------------------
## About this configuration
<> rdfs:label "Joseki Configuration File" .
## --------------------------------------------------------------
## About this server
[] rdf:type joseki:Server ;
joseki:serverDebug "true" ;
# Example of some initialization code.
joseki:initialization
[ module:implementation
[ module:className <java:org.joseki.util.ServiceInitSimple> ;
rdfs:label "Example initializer" ; ]
] ;
.
## --------------------------------------------------------------
## Services
## Services are the points that request are sent to.
## serviceRef that will be used to match requests to services,
## not some resource URI for the description.
## Note that the service reference and the routing of incoming
## requests by URI as defined by web.xml have to align.
# Service 1
# General purpose SPARQL processor, no dataset, expects the
# request to specify the dataset (either by parameters in the
# protocol request or in the query itself).
[]
rdf:type joseki:Service ;
rdfs:label "service point";
joseki:serviceRef "sparql" ;
joseki:processor joseki:ProcessorSPARQL;
joseki:dataset <#ds1> ;
.
## --------------------------------------------------------------
# Service 2 - SPARQL processor only handling a given dataset
[]
rdf:type joseki:Service ;
rdfs:label "SPARQL on the VIVO model" ;
joseki:serviceRef "VIVOService" ;
# web.xml just route this name to Joseki
# dataset part
joseki:dataset <#ds1> ;
# Service part.
# This processor will not allow either the protocol,
# nor the query, to specify the datset.
joseki:processor joseki:ProcessorSPARQL_FixedDS ;
.
## --------------------------------------------------------------
## Datasets
<#ds1> rdf:type ja:RDFDataset ;
ja:defaultGraph <#modelDB1> ;
rdfs:label "Dataset 1" ;
ja:namedGraph
[ ja:graphName <http://vitro.mannlib.cornell.edu/default/vitro-kb-2> ;
ja:graph <#modelDB1> ] ;
.
## --------------------------------------------------------------
# This is very very bad. Configure MySQL security correctly
## --------------------------------------------------------------
## --------------------------------------------------------------
<#modelDB1> rdf:type ja:RDBModel ;
ja:connection
[
ja:dbType "MySQL" ;
ja:dbURL <jdbc:mysql://localhost/vitro> ;
ja:dbUser "root" ;
ja:dbPassword "vitro123" ;
ja:dbClass "com.mysql.jdbc.Driver" ;
] ;
ja:reificationMode ja:minimal ;
## Minimal means fastpath is possible.
ja:modelName "http://vitro.mannlib.cornell.edu/default/vitro-kb-2"
.
## --------------------------------------------------------------
## Processors
joseki:ProcessorSPARQL
rdfs:label "General SPARQL processor" ;
rdf:type joseki:Processor ;
module:implementation joseki:ImplSPARQL ;
# Parameters - this processor processes FROM/FROM NAMED
joseki:allowExplicitDataset "true"^^xsd:boolean ;
joseki:allowWebLoading "true"^^xsd:boolean ;
## And has no locking policy (it loads data each time).
## The default is mutex (one request at a time)
joseki:lockingPolicy joseki:lockingPolicyNone ;
.
joseki:ProcessorSPARQL_FixedDS
rdfs:label "SPARQL processor for fixed datasets" ;
rdf:type joseki:Processor ;
module:implementation joseki:ImplSPARQL ;
# This processor does not accept queries with FROM/FROM NAMED
joseki:allowExplicitDataset "false"^^xsd:boolean ;
joseki:allowWebLoading "false"^^xsd:boolean ;
joseki:lockingPolicy joseki:lockingPolicyMRSW ;
.
# WARNING!!!! If you don't want people to update see wiki
# WARNING!!!! See how to add filter to block update proc.
joseki:ProcessorSPARQLUpdate
rdfs:label "SPARQL Update processor" ;
rdf:type joseki:Processor ;
module:implementation joseki:ImplSPARQLUpdate ;
joseki:lockingPolicy joseki:lockingPolicyMRSW ;
.
joseki:ImplSPARQL
rdf:type joseki:ServiceImpl ;
module:className
<java:org.joseki.processors.SPARQL>
.
joseki:ImplSPARQLUpdate
rdf:type joseki:ServiceImpl ;
module:className
<java:org.joseki.processors.SPARQLUpdate>
.
# Local Variables:
# tab-width: 4
# indent-tabs-mode: nil
# End:
|
Backup the config file
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo cp joseki-config.ttl joseki-config.default |
Make the new Joseki config file
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo touch joseki-config-vivo.ttl |
Edit the config file
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo nano joseki-config-vivo.ttl |
Copy and paste the following to the newly created Joseki VIVO config file
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix module: <http://joseki.org/2003/06/module#> .
@prefix joseki: <http://joseki.org/2005/06/configuration#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix sdb: <http://jena.hpl.hp.com/2007/sdb#> .
<> rdfs:label "Joseki Configuration File - SDB example" .
# Stripped down to support one service that exposes an
# SDB store as a SPARQL endpoint for query and one for
# one of the graphs in an SDB store.
[] rdf:type joseki:Server .
## --------------------------------------------------------------
## Services
# Service publishes the whole of the SDB store - this is the usual way to use SDB.
<#service1>
rdf:type joseki:Service ;
rdfs:label "SPARQL-SDB" ;
joseki:serviceRef "sparql" ; # web.xml must route this name to Joseki
joseki:dataset <#sdb-part> ;
joseki:processor joseki:ProcessorSPARQL_FixedDS ;
.
#to support connections using Sesame's HTTPRepository
<#service2>
rdf:type joseki:Service ;
rdfs:label "SPARQL-SDB" ;
joseki:serviceRef "sparql/repositories/" ; # web.xml must route this name to Joseki
joseki:dataset <#sdb-part> ;
joseki:processor joseki:ProcessorSPARQL_FixedDS ;
.
# Service that publishes part of an SDB store.
## <#service2>
## rdf:type joseki:Service ;
## rdfs:label "SPARQL-SDB (alt)" ;
## joseki:serviceRef "sparql/graph" ; # web.xml must route this name to Joseki
## joseki:dataset <#sdb-part> ;
## joseki:processor joseki:ProcessorSPARQL_FixedDS ;
## .
## SPARQL/Update.
## Creation of named graph from web requests is not supported.
<#serviceUpdate>
rdf:type joseki:Service ;
rdfs:label "SPARQL/Update" ;
joseki:serviceRef "update/service" ;
# dataset part
joseki:dataset <#sdb>; # Same as service1
joseki:processor joseki:ProcessorSPARQLUpdate
.
## --------------------------------------------------------------
## Datasets
## See also SDB documentation -- http://jena.hpl.hp.com/wiki/SDB
## Special declarations to cause SDB to be used.
## Initialize SDB.
## Tell the system that sdb:DatasetStore is an implementation of ja:RDFDataset .
## Tell the system that sdb:Model is an implementation of ja:RDFDataset .
[] ja:loadClass "com.hp.hpl.jena.sdb.SDB" .
sdb:DatasetStore rdfs:subClassOf ja:RDFDataset .
sdb:Model rdfs:subClassOf ja:Model .
<#sdb> rdf:type sdb:DatasetStore ;
## Number of concurrent connections allowed to this dataset.
joseki:poolSize 64 ;
sdb:store <#store> .
<#store> rdf:type sdb:Store ;
rdfs:label "SDB" ;
sdb:layout "layout2" ;
sdb:connection
[ rdf:type sdb:SDBConnection ;
## sdb:sdbType "postgresql" ;
## sdb:sdbHost "localhost" ;
## sdb:sdbName "SDB" ;
# Using Apache Derby
sdb:sdbHost "databasehost.my.edu" ;
sdb:sdbType "MySQL" ;
sdb:sdbName "databasename" ;
sdb:sdbUser "databaseuser" ;
sdb:sdbPassword "databasepassword" ;
sdb:driver "com.mysql.jdbc.Driver" ;
]
.
# Pick one graph out of the SDB store.
# Do not assemble the whole of the store this way - it is less efficient for that.
<#sdb-part> rdf:type ja:RDFDataset ;
# If ja:namedGraph is used here, there is no correspondence
# with the name in the SDB store.
ja:defaultGraph <#sdb-one-graph> ;
.
<#sdb-one-graph> a sdb:Model ;
sdb:dataset <#sdb> ;
# Uncomment to pick out a named graph from the store.
# If no "sdb:namedGraph" appearsm the store's default graph is used.
# is used as default graph of the dataset publically visible.
#sdb:graphName <http://example/aNamedGraph> ;
# Or even the merge of all named graphs
sdb:graphName <urn:x-arq:UnionGraph> ;
.
## --------------------------------------------------------------
## Processors
joseki:ProcessorSPARQL_FixedDS
rdfs:label "SPARQL processor for fixed datasets" ;
rdf:type joseki:Processor ;
module:implementation
[ rdf:type joseki:ServiceImpl ;
module:className <java:org.joseki.processors.SPARQL>
] ;
# This processor does not accept queries with FROM/FROM NAMED
joseki:allowExplicitDataset "false"^^xsd:boolean ;
joseki:allowWebLoading "false"^^xsd:boolean ;
# The database is safe for MRSW (multiple-reader, single-writer).
# joseki:lockingPolicy joseki:lockingPolicyMRSW ;
# recommended locking policy when not using SDB connection pooling
# joseki:lockingPolicy joseki:lockingPolicyMutex ;
joseki:lockingPolicy joseki:lockingPolicyNone ;
.
#joseki:ProcessorSPARQLUpdate
# rdfs:label "SPARQL Update processor" ;
# rdf:type joseki:Processor ;
# module:implementation
# [ rdf:type joseki:ServiceImpl ;
# module:className <java:org.joseki.processors.SPARQLUpdate>
# ] ;
# joseki:lockingPolicy joseki:lockingPolicyMRSW ;
# recommended locking policy when not using SDB connection pooling
# joseki:lockingPolicy joseki:lockingPolicyMutex ;
# joseki:lockingPolicy joseki:lockingPolicyNone ;
# .
# Local Variables:
# tab-width: 4
# indent-tabs-mode: nil
# End: |
Modify the configuration for connection to the database:
sdb:sdbHost "databasehost.my.edu" ;
sdb:sdbType "MySQL" ;
sdb:sdbName "databasename" ;
sdb:sdbUser "databaseuser" ;
sdb:sdbPassword "databasepassword" ;
sdb:driver "com.mysql.jdbc.Driver" ;
|
Save and exit using:
ctrl-x
Replace the default config with the new VIVO config
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo cp joseki-config-vivo.ttl joseki-config.ttl
Change directory into lib
vitro@vivo:/usr/local/Joseki-3.4.2$ cd lib
Download the mysql connector
Unzip the connector
mv index.html mysql-connector-java-5.0.8.zip |
Move the jar file up into the lib directory
cp mysql-connector-java-5.0.8/mysql-connector-java-5.0.8-bin.jar /usr/local/joseki/lib/Download the mysql connector |
Shut down the virtual appliance
vitro@vivo:/usr/local/Joseki-3.4.2/lib$ sudo shutdown -h now
You may need to open ports for 2020 in your own environment. In our example VM system you need to run the following comands to allow access from your computer to the virtual machine guest. This is simliar to the commands for opening port 8080 in the VIVO VM setup instructions. THERE ARE NO LINEBREAKS IN THESE COMMANDS.
Mylocalmachine$ VBoxManage setextradata "<NAME OF YOUR VM HERE IF YOU CHANGED IT>" "VBoxInternal/Devices/pcnet/0/LUN#0/Config/sparql/GuestPort" 2020
Mylocalmachine$VBoxManage setextradata "<NAME OF YOUR VM HERE IF YOU CHANGED IT>" "VBoxInternal/Devices/pcnet/0/LUN#0/Config/sparql/HostPort" 2020
Mylocalmachine$VBoxManage setextradata "<NAME OF YOUR VM HERE IF YOU CHANGED IT>" "VBoxInternal/Devices/pcnet/0/LUN#0/Config/sparql/Protocol" TCP
Restart the virtual appliance and login at the command prompt
Change directory to the Joseki root
vitro@vivo:/$ cd /usr/local/Joseki-3.4.2
Start the Joseki server to make sure its working ( set JOSEKIROOT NOW )
vitro@vivo:/usr/local/Joseki-3.4.2$ sudo JOSEKIROOT=/usr/local/Joseki-3.4.2 ./bin/rdfserver
Go to your local web browser and enter the following URL:
http://localhost:2020
If everything is working correctly, you will see the SPARQL generic home page for Joseki. You can now execute a
sample query by entering the following into the form:
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX core: <http://vivoweb.org/ontology/core#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?facultyname ?collegeName
WHERE
{
?a rdf:type core:Faculty .
?a rdfs:label ?facultyname .
?a ?pred ?c .
?c rdf:type core:College .
?c rdfs:label ?collegeName
}
ORDER BY ASC(?facultyname)
LIMIT 10 |
Sample Startup script file called "joskei" in (for debian): /etc/init.d/ |
#!/bin/bash
#/etc/init.d/joseki
PIDFILE=/var/run/joseki.pid
LOGFILE=/var/log/joseki.log
NAME=joseki
# Carry out specific functions when asked to by the system
case "$1" in
start)
if [ ! -f $PIDFILE ]; then
echo "Starting $NAME"
export JOSEKIROOT=/usr/local/joseki
cd /usr/local/joseki
/usr/local/joseki/bin/rdfserver &> $LOGFILE & echo $! > $PIDFILE
else
echo "$NAME already running"
fi
;;
stop)
echo "Stopping $NAME"
start-stop-daemon --stop --pidfile $PIDFILE
rm $PIDFILE
;;
restart)
echo "Restarting $NME"
$0 stop && sleep 5
$0 start
;;
*)
echo "Usage: /etc/init.d/joseki {start|stop|restart}"
exit 1
;;
esac
exit 0
|
( disables anonymous access to the Joseki Update Service) |
Thanks to: http://www.mediawiki.org/wiki/User:Alfredas/JosekiSecurity
In order to restrict access to the Joseki update service and make it accessible only from localhost:
|
<!-- Access Filter -->
<filter>
<filter-name>AccessFilter</filter-name>
<filter-class>nl.tudelft.tbm.servletaccessfilter.ServletAccessFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>AccessFilter</filter-name>
<url-pattern>/update/service/*</url-pattern>
</filter-mapping>
|
|
package nl.tudelft.tbm.servletaccessfilter;
import java.io.IOException;
import javax.servlet.Filter;
import javax.servlet.FilterChain;
import javax.servlet.FilterConfig;
import javax.servlet.ServletException;
import javax.servlet.ServletRequest;
import javax.servlet.ServletResponse;
import javax.servlet.http.HttpServletResponse;
public class ServletAccessFilter implements Filter {
@Override
public void destroy() {
}
@Override
public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain) throws IOException, ServletException {
if (request.getRemoteAddr().equals("0:0:0:0:0:0:0:1") || request.getRemoteAddr().equals("127.0.0.1")) {
chain.doFilter(request, response);
} else {
HttpServletResponse httpr = (HttpServletResponse) response;
httpr.sendError(HttpServletResponse.SC_FORBIDDEN);
}
}
@Override
public void init(FilterConfig config) throws ServletException {
}
}
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