[Mulgara-general] Unable to load a Krule file into Mulgara
Ghazzaoui, Ramez (NIH/NLM/LHC) [C]
ghazzaouir at mail.nih.gov
Fri Mar 21 13:19:28 PDT 2008
Thank you for pointing out the empty argument at the end of the
constrain conjunction. I removed it and the problem persists. Same error
message from Java.
-Ramez
_______________________________
Ramez Ghazzaoui
Contractor
NIH/NLM/LHC/CgSB/MOR
+1 (301) 435-3161
-----Original Message-----
From: Paul Gearon [mailto:gearon at ieee.org]
Sent: Friday, March 21, 2008 4:14 PM
To: Mulgara General
Subject: Re: [Mulgara-general] Unable to load a Krule file into Mulgara
I think it got upset with your empty argument at the end of the
constraint. Remove that and let me know.
I've added a new ticket for it:
http://mulgara.org/files/v1.1.1/mulgara-1.1.1-src.tar.gz
It will be some time before I can get back to it, but we expect to
automatically write these krule files in future, building them from a
more logic-like syntax. I've already built the parser, but I don't
have time to integrate it at the moment. When it's finally done,
you'd write your query like this:
owl:sameAs(name1, name2) :- bp:SHORT-NAME(name1, value),
bp:SHORT-NAME(name2, value).
Actually, I already have the OWL rule for that, which looks like:
owl:sameAs(x,y) :- a(x,z), a(y,z), owl:InverseFunctionalProperty(a).
In which case, you'll get your effect by declaring:
owl:InverseFunctionalProperty(bp:SHORT-NAME).
This can all be said in Krule, but the translation is verbose (as I'm
sure you've already seen), which is why I wrote the new logic-style
parser in the first place.
Paul
On Fri, Mar 21, 2008 at 12:38 PM, Ghazzaoui, Ramez (NIH/NLM/LHC) [C]
<ghazzaouir at mail.nih.gov> wrote:
> Hi,
>
> I am having trouble loading a rather simple Krule into Mulgara. Below
> are the details about what I am doing and what the error is. I wonder
if
> anyone here knows how to work around this problem.
> Thanks!
> -Ramez
>
>
> I created my model and loaded the triples successfully with this:
> -----------------------------------------------------------------
> create <rmi://localhost/server1#nida_1>;
> load <file:/export/home/moradmin/mulgara/raw_triples/nida_triples.nt>
> into <rmi://localhost/server1#nida_1>;
>
>
> Now I am trying to create an entailed Krule model with these Commands
> (which worked in the past on other models, other rules):
> ---------------------------------------------------------------------
> create <rmi://localhost/server1#krm_nida_sameAs>;
> create <rmi://localhost/server1#nida_1_ent_sameAs>;
>
> load <file:/export/home/moradmin/mulgara/rules/krm_nida_sameAs.rdf>
> into <rmi://localhost/server1#krm_nida_sameAs>;
>
> apply <rmi://localhost/server1#krm_nida_sameAs>
> to <rmi://localhost/server1#nida_1>
> <rmi://localhost/server1#nida_1_ent_sameAs>;
>
>
> I get this error:
> -----------------
>
> 2008-03-21 11:00:04,233 ERROR KruleLoader -
> Unexpected error during loading: null
> java.lang.NullPointerException
> at
> org.mulgara.krule.KruleLoader.getConstraints(KruleLoader.java:1003)
> at
> org.mulgara.krule.KruleLoader.getConstraints(KruleLoader.java:1014)
> at org.mulgara.krule.KruleLoader.loadJoinConstraints
> (KruleLoader.java:863)
> at
org.mulgara.krule.KruleLoader.loadRdfObjects(KruleLoader.java:317)
> at org.mulgara.krule.KruleLoader.readRules(KruleLoader.java:254)
> at org.mulgara.resolver.DatabaseSession.buildRules
> (DatabaseSession.java:508)
> at org.mulgara.server.rmi.SessionWrapperRemoteSession.buildRules
> (SessionWrapperRemoteSession.java:461)
> at sun.reflect.GeneratedMethodAccessor19.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke
> (DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:585)
> at
> sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:294)
> at sun.rmi.transport.Transport$1.run(Transport.java:153)
> at java.security.AccessController.doPrivileged(Native Method)
> at sun.rmi.transport.Transport.serviceCall(Transport.java:149)
> at sun.rmi.transport.tcp.TCPTransport.handleMessages
> (TCPTransport.java:460)
> at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run
> (TCPTransport.java:701)
> at java.lang.Thread.run(Thread.java:595)
> Syntax error (line 16): org.mulgara.rules.InitializerException:
> Unexpected error loading rules
>
>
> The Krule file (krm_nida_sameAs.rdf) is as follows:
> ---------------------------------------------------
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE rdf:RDF [
> <!ENTITY owl "http://www.w3.org/2002/07/owl#">
> <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
> <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
> <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
> <!ENTITY mulgara "http://mulgara.org/mulgara#">
> <!ENTITY krule "http://mulgara.org/owl/krule/#">
> <!ENTITY bp "http://www.biopax.org/release/biopax-level2.owl#">
> ]>
>
> <rdf:RDF xmlns:rdf="&rdf;"
> xmlns:rdfs="&rdfs;"
> xmlns:owl="&owl;"
> xmlns:xsd="&xsd;"
> xmlns="&krule;"
> xmlns:krule="&krule;"
> xmlns:bp="&bp;"
> xml:base="http://mulgara.org/owl/krule/">
>
> <krule:URIReference rdf:about="#bp_short_name">
> <rdf:value rdf:resource="bp:SHORT-NAME"/>
> </krule:URIReference>
>
> <krule:URIReference rdf:about="#owl_sameAs">
> <rdf:value rdf:resource="owl:sameAs"/>
> </krule:URIReference>
>
> <Variable rdf:about="#name1">
> <name>name1</name>
> </Variable>
>
> <Variable rdf:about="#name2">
> <name>name2</name>
> </Variable>
>
> <Variable rdf:about="#value">
> <name>value</name>
> </Variable>
>
> <!-- * plain sameAs -->
> <krule:Rule rdf:about="#same_as">
> <hasQuery>
> <Query>
> <selectionVariables>
> <rdf:Seq>
> <rdf:li rdf:resource="#name1"/>
> <rdf:li rdf:resource="owl_sameAs"/>
> <rdf:li rdf:resource="#name2"/>
> </rdf:Seq>
> </selectionVariables>
> <hasWhereClause>
> <ConstraintConjunction>
>
> <argument>
> <SimpleConstraint>
> <hasSubject>
> <Variable rdf:about="#name1"/>
> </hasSubject>
> <hasPredicate>
> <URIReference rdf:about="#bp_short_name"/>
> </hasPredicate>
> <hasObject>
> <Variable rdf:about="#value"/>
> </hasObject>
> </SimpleConstraint>
> </argument>
>
> <argument>
> <SimpleConstraint>
> <hasSubject>
> <Variable rdf:about="#name2"/>
> </hasSubject>
> <hasPredicate>
> <URIReference rdf:about="#bp_short_name"/>
> </hasPredicate>
> <hasObject>
> <Variable rdf:about="#value"/>
> </hasObject>
> </SimpleConstraint>
> </argument>
>
> <argument>
> </argument>
>
> </ConstraintConjunction>
> </hasWhereClause>
> </Query>
> </hasQuery>
> </krule:Rule>
>
> </rdf:RDF>
>
>
>
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