They don't have an inference layer because they do all the inference off the triple store using https://github.com/NatLibFi/Skosify . I didn't know that and I tried first with inference because I thought that Jena would be able to provide inferred types for SKOS.
Used SKOS owl was the one from the standard https://www.w3.org/2004/02/skos/vocabs The problem is that I cannot share my SKOS vocabulary but I guess the problem should be reproducible by: - loading skos.rdf - loading a big SKOS taxonomy - running the CONSTRUCT query above in a server with the following config.ttl @prefix tdb2: <http://jena.apache.org/2016/tdb#> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix fuseki: <http://jena.apache.org/fuseki#> . :service_tdb_all a fuseki:Service ; rdfs:label "TDB2 example-inf" ; fuseki:dataset :dataset ; fuseki:name "example" ; fuseki:serviceQuery "query" , "" , "sparql" ; fuseki:serviceReadGraphStore "get" ; fuseki:serviceReadQuads "" ; fuseki:serviceReadWriteGraphStore "data" ; fuseki:serviceReadWriteQuads "" ; fuseki:serviceUpdate "" , "update" ; fuseki:serviceUpload "upload" . :tdb_dataset_readwrite a tdb2:DatasetTDB2 ; tdb2:location "example" ; . :dataset a ja:RDFDataset ; ja:defaultGraph :model_inf . :model_inf a ja:InfModel ; ja:baseModel :graph . ja:reasoner [ ja:reasonerURL <http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner > ] . :graph rdf:type tdb2:GraphTDB ; tdb2:dataset :tdb_dataset_readwrite ; On Thu, 4 Mar 2021 at 12:33, Andy Seaborne <a...@apache.org> wrote: > Osma's tutorial > > https://github.com/NatLibFi/Skosmos/wiki/InstallTutorial > > doesn't have an inference layer. > > Looks like the fact its skosmos is not a factor and it is the rest of > the setup. > > Andy > > On 04/03/2021 11:22, Andy Seaborne wrote: > > > > > > On 04/03/2021 11:10, Toni Cebrián wrote: > >> Hi Andy, > >> > >> Fuseki server was 3.14.0. I didn't include the full stack trace > >> because > >> it was clear that it is just a timeout. > > > > It would help me to know what part of the Fuseki engine this is > > happening in. > > > > There was a change for better diagnostics for > > org.eclipse.jetty.io.EofException but I can't tell if this is on that > > path or another. > > > >> This timeout happens because the > >> reasoner hogs the server without completing the query. I asked in the > >> Skosmos user group > >> (https://groups.google.com/g/skosmos-users/c/bSzpAhdprvY) > >> and the solution was to materialise all relationships before hand and > >> remove reasoning from Jena. > >> But to me, performing inference on the skos ontology should be pretty > >> straightforward even for online querying, shouldn't it? What am I doing > >> wrong so a simple query works in milliseconds when I materialise all > >> relations myself but cannot be handled by the most lightweight OWL > >> reasoner? > > > > It is only the first query. That's when initialization happens. > > > > 4597 sounds very small but I don't know skosmos. > > > > What does the OWL look like? > > > > And the data - because there may be a lot of other inference because > > OWLMicro is general and not specific to SKOS. Some rules are expensive. > > > > And if it large and cold off disk, then, something else is involved. > > > > Maybe you want a SKOS specific rule set? > > > > What is in the Fuseki configuration file? > > > > Andy > > > >> > >> Toni > >> > >> On Tue, 2 Mar 2021 at 15:49, Andy Seaborne <a...@apache.org> wrote: > >> > >>> Hi Toni, > >>> > >>> Which version of Fuseki is this? > >>> What's the full stacktrace? (the operation isn't showing below) > >>> > >>> The exception usually means client has gone away before the request > >>> response is finished. (Sometimes, that's an intermediate like a > >>> proxy/reverse proxy.) > >>> > >>> Maybe the first query is expensive because it is doing all the rules > >>> setup. More a Skosmos question. > >>> > >>> Andy > >>> > >>> On 02/03/2021 09:07, Toni Cebrián wrote: > >>>> Hi, > >>>> > >>>> I'm trying to setup Fuseki with the Skosmos frontend ( > >>>> https://skosmos.org/) using docker images for both servers. > >>>> In Fuseki I've uploaded to the default graph the skos.rdf file > >>>> plus > >>> the > >>>> .ttl with my vocabulary comprising around 4597 concepts. Fuseki is > also > >>>> setup with MicroOWL reasoner: > >>>> > >>>> ja:reasonerURL <http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner> > >>>> > >>>> so I can navigate the SKOS taxonomy back and forth. > >>>> The problem is that the first query that Skosmos sends to Jena > >>>> never > >>>> returns: > >>>> > >>>> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> > >>>> CONSTRUCT { <http://example.org/MyScheme> ?property ?value . } > >>>> WHERE { > >>>> <http://example.org/MyScheme> ?property ?value . > >>>> FILTER (?property != skos:hasTopConcept) } > >>>> > >>>> After sending the query, one CPU goes 100% and after a while before > >>> getting > >>>> any results I can see this exception in fuseki: > >>>> > >>>> skosmos-fuseki | [2021-03-02 08:19:04] Fuseki INFO Exception > while > >>>> writing the response model: org.eclipse.jetty.io.EofException > >>>> skosmos-fuseki | org.apache.jena.atlas.RuntimeIOException: > >>>> org.eclipse.jetty.io.EofException > >>>> skosmos-fuseki | at > >>>> org.apache.jena.atlas.io.IO.exception(IO.java:261) > >>>> skosmos-fuseki | at > >>>> org.apache.jena.atlas.io > >>> .BufferingWriter.flushBuffer(BufferingWriter.java:136) > >>>> skosmos-fuseki | at > >>>> org.apache.jena.atlas.io.BufferingWriter.output(BufferingWriter.java:86) > > >>>> > >>>> skosmos-fuseki | at > >>>> org.apache.jena.atlas.io.BufferingWriter.write(BufferingWriter.java:173) > > >>>> > >>>> skosmos-fuseki | at > >>>> org.apache.jena.atlas.io.Writer2.print(Writer2.java:55) > >>>> skosmos-fuseki | at > >>>> org.apache.jena.riot.out.quoted.QuotedURI.writeURI(QuotedURI.java:46) > >>>> skosmos-fuseki | at > >>>> > >>> > org.apache.jena.riot.out.NodeFormatterNT.formatURI(NodeFormatterNT.java:46) > >>> > >>>> > >>>> > >>>> to me it doesn't look like a very complex query, so my questions are: > >>>> - Is Jena able to handle SKOS vocabularies in the range of thousand > >>>> terms > >>>> when inference is on? > >>>> - If so, how should I configure Fuseki to work with that dataset? > >>>> - Maybe related, but does anyone have a similar Skosmos setup where I > >>> could > >>>> borrow the Jena config files? > >>>> > >>>> Thanks > >>>> > >>> > >> >
