default (empty) prefix issue

[Conrad Leonard]

Hi;

I have an issue with a bean that is annotated with the following @Namespaces:

@Namespaces({"","http://purl.org/net/grafli#"

,"owl","http://www.w3.org/2002/07/owl#"

,"rdf","http://www.w3.org/1999/02/22-rdf-syntax-ns#"

,"xml","http://www.w3.org/XML/1998/namespace"

,"xsd","http://www.w3.org/2001/XMLSchema#"

,"foaf","http://xmlns.com/foaf/0.1/"

,"rdfs","http://www.w3.org/2000/01/rdf-schema#"

,"skos2","http://www.w3.org/2008/05/skos#"

})

When I run a query using the empty qname e.g.

aManager.createQuery("where {?result a :SequencingRun; :wasAssociatedWith [a foaf:Person; foaf:accountName 'JohnPe']}")

I get the exception:

java.lang.IllegalArgumentException: Invalid query: PREFIX skos2: <http://www.w3.org/2008/05/skos#>

PREFIX owl: <http://www.w3.org/2002/07/owl#>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

PREFIX xml: <http://www.w3.org/XML/1998/namespace>

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

PREFIX foaf: <http://xmlns.com/foaf/0.1/>

select ?result where {?result a :sequencingrun; :wasassociatedwith [a foaf:person; foaf:accountname 'johnpe']}

at com.clarkparsia.empire.impl.sparql.SPARQLDialect.validateQueryFormat(SPARQLDialect.java:111)

at com.clarkparsia.empire.impl.RdfQuery.<init>(RdfQuery.java:172)

at com.clarkparsia.empire.impl.RdfQueryFactory.newQuery(RdfQueryFactory.java:104)

at com.clarkparsia.empire.impl.RdfQueryFactory.createQuery(RdfQueryFactory.java:136)

at com.clarkparsia.empire.impl.EntityManagerImpl.createQuery(EntityManagerImpl.java:254)

at EmpireTest.main(wrapper.groovy:31)

Caused by: org.openrdf.query.MalformedQueryException: org.openrdf.query.parser.sparql.ast.VisitorException: QName ':sequencingrun' uses an undefined prefix

From the trace it looks like the constructed query is missing the line I would expect declaring the empty qname, i.e.

PREFIX : <http://purl.org/net/grafli#>

so it is not being registered when the beans are inspected, or something? I tried moving that prefix/namespace pair to different location in the @Namespaces initializer but to no avail.  Am I doing something unexpected?

Thanks for Empire, b.t.w; it's a great library.

[Mike Grove]

No, that ought to work.  I guess it's eating it because it's the default namespace.  If you give it a specific prefix, does it work?

 

Thanks for Empire, b.t.w; it's a great library.

Thanks!

Mike

 

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[Conrad Leonard]

Hi Mike;

Yes, if I give the namespace anything other than the empty prefix name, the query is constructed correctly with the appropriate @PREFIX statement, and returns results.

[Mike Grove]

Ah, ok.  Thanks for pointing this out.

I've created an issue for this [1].

Cheers,

Mike

[1] https://github.com/mhgrove/Empire/issues/94

[Conrad Leonard]

Inspecting the contents of PrefixManager.GLOBAL immediately before constructing the query, the default namespace (empty prefix) is certainly present; I think the immediate cause of its absence in the constructed query is the block that explicitly excludes the empty prefix in

com.clarkparsia.empire.impl.sparql.SPARQLDialect.insertNamespaces():

        if (aPrefix.trim().equals("")) {
                continue;
        }

But I don't know why that is there so I'm not going to mess with it :)

in com.clarkparsia.empire.impl.sparql.SPARQLDialect.insertNamespaces()