I want to run this query on my Joseki instance but after a while Joseki stops transmitting any more data.

PREFIX rdf: _http://www.w3.org/1999/02/22-rdf-syntax-ns#_ 
PREFIX wb: _http://purl.uniprot.org/wormbase/_
prefix rdfs:     _http://www.w3.org/2000/01/rdf-schema#_

SELECT ?ep ?up_gene ?at ?at_desc ?ls WHERE {
    ?ep a _http://manuels/wip/2013/wormbase.org/wormmart/expression_pattern_ .
    ?ep _http://manuels/wip/2013/wormbase.org/wormmart/expressed_gene_ ?gene .
    ?ep _http://manuels/wip/2013/wormbase.org/wormmart/anatomy_term_  ?at .
    ?ep _http://manuels/wip/2013/wormbase.org/wormmart/life_stage_  ?ls .
    ?at rdfs:label ?at_desc
  } .
  SERVICE _http://localhost:2020/celegans_ {
    ?connection _http://purl.uniprot.org/core/transcribedFrom_ ?gene .
    ?connection a _http://purl.uniprot.org/core/Transcript_Resource_ .
    ?up_gene a _http://purl.uniprot.org/core/Protein_ .
    ?up_gene ?rel ?connection .
  } .

I can see in the logs of Joseki that it runs several queries on localhost:2020/celegans like this one:

12:27:42 INFO  SPARQL               :: OK/select: SELECT  * WHERE   { ?connection  _http://purl.uniprot.org/core/transcribedFrom_  _http://purl.uniprot.org/wormbase/WBGene00009888_ ;               _http://www.w3.org/1999/02/22-rdf-syntax-ns#type_  _http://purl.uniprot.org/core/Transcript_Resource_ .     ?up_gene  _http://www.w3.org/1999/02/22-rdf-syntax-ns#type_  _http://purl.uniprot.org/core/Protein_ ;               ?rel                  ?connection .   }

but after about 10 seconds it stops: not data is received by the browser or wget anymore and no more queries appear in the logs. However, the HTTP connection is not closed and only about 25kb of data is sent so I expect that the full query has not finished, yet.

What might cause this?

PS: I replaced all smaller-than and larger-than chars by underscores (_) in this post because markdown didn't like them

asked 14 Jan '13, 06:41

foobar's gravatar image

accept rate: 0%

Hmmm, the amount of data that is transferred is always 24576 bytes. interesting...

(14 Jan '13, 06:49) foobar foobar's gravatar image

This looks like an issue that is fixed in Fuseki. Joseki is replaced by Fuseki. Try using the latest release of Fuseki.

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answered 14 Jan '13, 09:17

AndyS's gravatar image

AndyS ♦
accept rate: 33%

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question asked: 14 Jan '13, 06:41

question was seen: 696 times

last updated: 14 Jan '13, 09:17