Great! I finally have it all working.
Here's the crucial parts of the joseki-config.ttl
%%%%%%%%%%
[] ja:loadClass "com.hp.hpl.jena.sdb.SDB" .
sdb:DatasetStore rdfs:subClassOf ja:RDFDataset .
sdb:Model rdfs:subClassOf ja:Model .
<#mydata> rdf:type sdb:DatasetStore ;
joseki:poolSize 5 ; # Number of concurrent connections
allowed to this dataset.
sdb:store <#store> .
<#store> rdf:type sdb:Store ;
rdfs:label "SDB";
sdb:layout "layout2";
sdb:connection
[ rdf:type sdb:SDBConnection;
sdb:sdbType "mysql" ;
sdb:sdbHost "localhost:3306" ;
sdb:sdbUser "" ; #omitted
sdb:sdbPassword "" ; #omitted
sdb:sdbName "" ; #omitted
sdb:driver "com.mysql.jdbc.Driver" ;
]
.
%%%%%%%%%%
One of the issues I had was that in my mySql database, I was using
Jena models, with tables such as jena-stmts, jena-models etc... Now
that I am using SDB datastore, I now have 4 mySql tables: Nodes,
Prefixes, Quads, Triples (which feels much nicer).
I used this Java to setup an SDB datastore:
%%%
String className = "com.mysql.jdbc.Driver";
Class.forName(className); // Load the Driver
String DB_URL = "jdbc:mysql://localhost/DB"; // URL of database
String DB_USER = ""; // database user id
String DB_PASSWD = ""; // database password
SDBConnection conn = new SDBConnection(DB_URL, DB_USER, DB_PASSWD);
StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash,
DatabaseType.MySQL) ;
Store store = SDBFactory.connectStore(conn,storeDesc);
store.getTableFormatter().create();
store.close();
%%%
My only issue now is that the Joseki connection to my database becomes
idle and keeps timing out, with this error message:
No operations allowed after connection closed.Connection was
implicitly closed by the driver.
Previously, I used:
ja:dbURL "jdbc:mysql://localhost/MyDB?autoReconnect=true" ;
Is there an alternative I can use in the sdb:sdbHost property, to
keep the connection alive, or auto-reconnect?
Many thanks,
--
Rob Stewart
On 19 May 2011 09:11, Andy Seaborne <[email protected]> wrote:
> TDB does not use a relational database - did you mean SDB?
>
> There's are examples of both in the Joseki download.
>
> TDB --------------
>
> [] ja:loadClass "com.hp.hpl.jena.tdb.TDB" .
> tdb:DatasetTDB rdfs:subClassOf ja:RDFDataset .
> tdb:GraphTDB rdfs:subClassOf ja:Model .
>
> ## ---- A whole dataset managed by TDB
> <#mydata> rdf:type tdb:DatasetTDB ;
> tdb:location "TDB" ;
> .
>
> SDB --------------
>
> [] ja:loadClass "com.hp.hpl.jena.sdb.SDB" .
> sdb:DatasetStore rdfs:subClassOf ja:RDFDataset .
> sdb:Model rdfs:subClassOf ja:Model .
>
> <#mydata> rdf:type sdb:DatasetStore ;
> ## Number of concurrent connections allowed to this dataset.
> joseki:poolSize 2 ;
> 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 "localhost" ;
> sdb:sdbType "derby" ;
> sdb:sdbName "DB/Derby" ;
> ]
> .
> -------------
>
> You want <#mydata>, as in your original Joseki config file, connecting to
> one of the places I have used it above.
>
> You do not want a ja:RDFDataset and identifying a specific model.
>
> Andy
>
>
> On 17/05/11 18:34, Rob Stewart wrote:
>>
>> Hi Andy,
>>
>> Unfortunately, joseki errors are very cryptic e.g.:
>>
>> WARN [http-8080-2] (Servlet.java:183) - Internal server error
>> java.lang.NullPointerException
>> at org.joseki.DatasetDesc.acquireDataset(DatasetDesc.java:78)
>>
>> I am now trying to use TDB as you recommended, but with no luck. My
>> configuration:
>>
>> %%%%%%%%%%
>> [] ja:loadClass "com.hp.hpl.jena.tdb.TDB" . ## Initialize TDB.
>> tdb:DatasetTDB rdfs:subClassOf ja:RDFDataset .
>> tdb:GraphTDB rdfs:subClassOf ja:Model .
>> <#dataset>
>> a ja:RDFDataset;
>> ja:defaultGraph [
>> a ja:InfModel;
>> ja:baseModel [
>> a tdb:GraphTDB;
>> ja:connection
>> [
>> ja:dbType "MySQL" ;
>> ja:dbURL "jdbc:mysql://localhost/MyDB?autoReconnect=true"
>> ;
>> ja:dbUser "" ;
>> ja:dbPassword "" ;
>> ja:dbClass "com.mysql.jdbc.Driver" ;
>> ] ;
>> ja:modelName "UserProfiles"
>> ];
>> ];
>> .
>>
>> <#service3>
>> rdf:type joseki:Service ;
>> rdfs:label "SPARQL-TDB" ;
>> joseki:serviceRef "sparql" ; # web.xml must route this name to Joseki
>> joseki:dataset<#dataset> ;
>> joseki:processor joseki:ProcessorSPARQL_FixedDS ;
>> .
>>
>> <#serviceUpdate>
>> rdf:type joseki:Service ;
>> rdfs:label "SPARQL/Update" ;
>> joseki:serviceRef "update/service" ;
>> # dataset part
>> joseki:dataset<#dataset>;
>> # Service part.
>> # This processor will not allow either the protocol,
>> # nor the query, to specify the dataset.
>> joseki:processor joseki:ProcessorSPARQLUpdate
>> .
>>
>> %%%%%%%%
>>
>> I'm not overly familiar with ttl syntax, but the errors given from
>> Joseki merely say "NullPointException", without reference to the
>> problem... ttl syntax? Database error? ja:modelName not found?
>>
>>
>> --
>> Rob
>>
>>
>>
>>
>>
>>
>>
>>
>> On 17 May 2011 11:13, Andy Seaborne<[email protected]> wrote:
>>>
>>> Sorry my misreading - but you are stil putting one SDB model into a
>>> general
>>> dataset. If you want to create new models, yo uneed to use a dataset.
>>> (untested):
>>>
>>> joseki:dataset<#mydata> ;
>>>
>>> <#mydata> rdf:type sdb:DatasetStore ;
>>> sdb:store<#store> .
>>>
>>> <#store> rdf:type sdb:Store ;
>>> rdfs:label "SDB" ;
>>> sdb:layout "layout2" ;
>>> sdb:connection ....
>>>
>>>
>>> (From joseki-config-sdb.ttl)
>>>
>>> http://openjena.org/wiki/SDB/Dataset_Description
>>>
>>> Andy
>>>
>>>
>>> On 17/05/11 10:42, Rob Stewart wrote:
>>>>
>>>> Hi Andy,
>>>>
>>>> Thanks for your input. I can't see in my configuration where I am
>>>> pointing to "RDB" at all... Could you highlight my error.
>>>>
>>>> Looking at the fragment below, I would have thought that I am indeed
>>>> using
>>>> SDB ?
>>>> %%%%%
>>>> _:ProfileDatabase rdf:type ja:SDBModel ;
>>>> ja:connection
>>>> [
>>>> ja:dbType "MySQL" ;
>>>> ja:dbURL "jdbc:mysql://localhost/MyDB?autoReconnect=true"
>>>> ;
>>>> ja:dbUser "" ;
>>>> ja:dbPassword "" ;
>>>> ja:dbClass "com.mysql.jdbc.Driver" ;
>>>> ] ;
>>>> ja:modelName "UserProfiles"
>>>> .
>>>> %%%%
>>>> thanks,
>>>>
>>>> Rob
>>>>
>>>> On 17 May 2011 10:28, Andy Seaborne<[email protected]>
>>>> wrote:
>>>>>
>>>>> Hi Rob,
>>>>>
>>>>> You have one model backed by Jena's old database layer (AKA RDB) in
>>>>> MySQL.
>>>>> That model is put into a general purpose, in-memory dataset.
>>>>>
>>>>> Any further models you create will be in-memory, not in MySQL.
>>>>>
>>>>> You need to use SDB or TDB to get a persistent dataset, rather than a
>>>>> single
>>>>> persistent model.
>>>>>
>>>>> Currently, DBS provides transactions; TDB scales better.
>>>>>
>>>>> Fuseki is "Joseki4" and may be easier to use for you.
>>>>>
>>>>> Andy
>>>>>
>>>>> On 17/05/11 01:25, Rob Stewart wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm currently having an issue with Joseki. I have created a mySql
>>>>>> database, and added 1 Jena model, with a small number of triples.
>>>>>>
>>>>>> I can SPARQL query them with the use of the sparql.html form, and I
>>>>>> receive all the of the results that I would expect. My problem is with
>>>>>> SPARQL Update, through the use of the update.html form.
>>>>>>
>>>>>> I can:
>>>>>> 1) CREATE GRAPH's
>>>>>> 2) INSERT DATA INTO these graphs
>>>>>> 3) Go to the sparql.html form, and query these inserted triples, in
>>>>>> each of these graphs. So - the data is going into memory.
>>>>>>
>>>>>> However - I am monitoring the mySql database as I run the INSERT INTO
>>>>>> calls, and no triples are added in `jena_g1t1_stmt', and no graphs are
>>>>>> added in `jena_graph'. Indeed, when I kill Joseki and restart it, all
>>>>>> of my inserted triples dissapear, and cannot be found with a SPARQL
>>>>>> query. Perhaps this is down to an incorrect configuration file? Here
>>>>>> it is, minus sensitive information:
>>>>>>
>>>>>> %%%%%%%%%%%%%%
>>>>>>
>>>>>> <#server> rdf:type joseki:Server ;
>>>>>> # Example of some initialization code.
>>>>>> joseki:initialization
>>>>>> [ module:implementation
>>>>>> [ module:className<java:org.joseki.util.ServiceInitSimple>
>>>>>> ;
>>>>>> rdfs:label "Example initializer" ; ]
>>>>>> ] ;
>>>>>> .
>>>>>>
>>>>>> <#mydata> rdf:type ja:RDFDataset ;
>>>>>> rdfs:label "DSpaceImage" ;
>>>>>> ja:defaultGraph _:ProfileDatabase
>>>>>> .
>>>>>>
>>>>>> _:ProfileDatabase rdf:type ja:SDBModel ;
>>>>>> ja:connection
>>>>>> [
>>>>>> ja:dbType "MySQL" ;
>>>>>> ja:dbURL
>>>>>> "jdbc:mysql://localhost/MyDB?autoReconnect=true"
>>>>>> ;
>>>>>> ja:dbUser "" ;
>>>>>> ja:dbPassword "" ;
>>>>>> ja:dbClass "com.mysql.jdbc.Driver" ;
>>>>>> ] ;
>>>>>> ja:modelName "UserProfiles"
>>>>>> .
>>>>>>
>>>>>> <#service1>
>>>>>> rdf:type joseki:Service ;
>>>>>> rdfs:label "service point" ;
>>>>>> joseki:serviceRef "sparql" ; # web.xml must route this name to
>>>>>> Joseki
>>>>>> joseki:processor joseki:ProcessorSPARQL ;
>>>>>> joseki:dataset<#mydata> ;
>>>>>> .
>>>>>>
>>>>>> <#serviceUpdate>
>>>>>> rdf:type joseki:Service ;
>>>>>> rdfs:label "SPARQL/Update" ;
>>>>>> joseki:serviceRef "update/service" ;
>>>>>> # dataset part
>>>>>> joseki:dataset<#mydata>;
>>>>>> # Service part.
>>>>>> # This processor will not allow either the protocol,
>>>>>> # nor the query, to specify the dataset.
>>>>>> joseki:processor joseki:ProcessorSPARQLUpdate
>>>>>> .
>>>>>>
>>>>>> <#serviceRead>
>>>>>> rdf:type joseki:Service ;
>>>>>> rdfs:label "SPARQL" ;
>>>>>> joseki:serviceRef "sparql/read" ;
>>>>>> # dataset part
>>>>>> joseki:dataset<#mydata> ; ## Same dataset
>>>>>> # Service part.
>>>>>> # This processor will not allow either the protocol,
>>>>>> # nor the query, to specify the dataset.
>>>>>> joseki:processor joseki:ProcessorSPARQL_FixedDS ;
>>>>>> .
>>>>>>
>>>>>> 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 ;
>>>>>> .
>>>>>>
>>>>>> 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> .
>>>>>>
>>>>>>
>>>>>> %%%%%%%%%%%%%%%
>>>>>>
>>>>>> Anything that I've missed? I'm also not sure whether to opt for SDB or
>>>>>> TDB, and what the implications of either, are?
>>>>>>
>>>>>> --
>>>>>> Rob Stewart
>>>>>
>>>
>
