Hi Ivan, I actually did have a problem earlier loading data, but deleted the containing graph and did not think that there would be consequences afterwards. As I recall, the error I got at the time was that the data was invalid (something like it only accepts rdf/xml, turtle,etc), but without providing any indication of which triples or what portion of the file had caused the problem. Since at this time I was only interested in a small portion of the triples, I parsed out the ones that I was interested, created a separate file with those, and loaded them using WebDav without (apparently) any problems.
The file I originally tried to load unsuccesfully was the OWL version of the GO ontology. The web page: http://www.geneontology.org/GO.downloads.ontology.shtml The file: http://archive.geneontology.org/latest-termdb/go_daily-termdb.owl.gz Let me know if you also want the subset I created. Too big for an attachment. Thanks for your help, Marco ________________________________ From: Ivan Mikhailov <imikhai...@openlinksw.com> To: Hugh Williams <hwilli...@openlinksw.com> Cc: Marco Ocana <marco.oc...@balboasystems.com>; virtuoso-users@lists.sourceforge.net Sent: Thursday, April 9, 2009 4:12:50 PM Subject: Re: [Virtuoso-users] Problem with xml and json format using sparql end-point Hello Marco, We can see the error "...bad id 258" (i.e., the very first non-default language remembered by the database) at your box, the fact of proper output "xml:lang": "en" and <literal xml:lang="en"> on other box and we can guess that "en" as the most popular language is good candidate for being the first language in the database. Were there any critical errors on loading your data to the database? It seems that the database is inconsistent. That's pretty strange and I'd like to know the sequence of actions that may cause this error. I.e., I know one sequence: a failed loading while the transaction log turned off. I don't know any other case. Best Regards, Ivan Mikhailov OpenLink Software http://virtuoso.openlinksw.com On Thu, 2009-04-09 at 18:40 +0100, Hugh Williams wrote: > Hi Marco, > > > I have load your data into Virtuoso 5.0.10.3037 instances on Mac OS X > and Windows and running the queries you provide I get the following: > > > Query: > > > http://localhost:8890/sparql/?query=%0Aprefix%20obo%3A%20%3Chttp% > 3A//purl.org/obo/owl/GO%23%3E%0Aprefix%20goformat%3A%20%3Chttp% > 3A//www.geneontology.org/formats/oboInOwl%23%3E%0Aprefix%20rdfs%3A%20% > 3Chttp%3A//www.w3.org/2000/01/rdf-schema%23%3E%0Aselect%20%3FmainName% > 0AFROM%20%3Chttp%3A//goOneProcess.com%3E%0Awhere%20{%0Aobo% > 3AGO_0006554%0Ardfs%3Alabel%20%3FmainName.%0A}&format=json > > > Returns: > > > { "head": { "link": [], "vars": ["mainName"] }, > "results": { "distinct": false, "ordered": true, "bindings": [ > { "mainName": { "type": "literal", "xml:lang": "en", "value": > "lysine catabolic process" }} ] } } > > > Query: > > > http://localhost:8890/sparql/?query=%0Aprefix%20obo%3A%20%3Chttp% > 3A//purl.org/obo/owl/GO%23%3E%0Aprefix%20goformat%3A%20%3Chttp% > 3A//www.geneontology.org/formats/oboInOwl%23%3E%0Aprefix%20rdfs%3A%20% > 3Chttp%3A//www.w3.org/2000/01/rdf-schema%23%3E%0Aselect%20%3FmainName% > 0AFROM%20%3Chttp%3A//goOneProcess.com%3E%0Awhere%20{%0Aobo% > 3AGO_0006554%0Ardfs%3Alabel%20%3FmainName.%0A}&format=json > > > Returns: > > > <?xml version="1.0" ?> > <sparql xmlns="http://www.w3.org/2005/sparql-results#"; > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; > xsi:schemaLocation="http://www.w3.org/2001/sw/DataAccess/rf1/result2.xsd";> > <head> > <variable name="mainName"/> > </head> > <results distinct="false" ordered="true"> > <result> > <binding name="mainName"><literal xml:lang="en">lysine catabolic > process</literal></binding> > </result> > </results> > </sparql> > > > Thus I cannot recreate the problem, are these the results you would > expect ? > > > Is your server "http://www.mysparlendpoint.com:8890/"; not accessible > remotely as the server fails to load when I run it ? > > > Best Regards > Hugh Williams > Professional Services > OpenLink Software > Web: http://www.openlinksw.com > Support: http://support.openlinksw.com > Forums: http://boards.openlinksw.com/support > > > > > > On 9 Apr 2009, at 16:09, Marco Ocana wrote: > > > Hi, > > > > I am running Virtuoso open-source edition Version 5.0.10.3037 on > > Windows XP 32-Bit. > > I imported a subset of the GO Ontology, OWL version using the WebDAV > > mechanism in the Conductor. > > When I use the SPARQL endpoint to do some simple queries, the HTML > > table format returns to the browser the expected results. However, > > if I specify the json format or xml format in the query URL, I get > > errors. Any help resolving this problem would be greatly > > appreciated. Below are the details. > > > > Marco Ocana > > Balboa Systems, Inc. > > > > I have attached a subset of my dataset (about 70 triples) that > > reproduces the problem. These I imported into a graph called: > > http://goOneProcess.com > > > > The unescaped query: > > > > prefix obo: <http://purl.org/obo/owl/GO#> > > prefix goformat: <http://www.geneontology.org/formats/oboInOwl#> > > prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> > > select ?mainName > > FROM <http://goOneProcess.com> > > where { > > obo:GO_0006554 rdfs:label ?mainName. > > } > > > > The query URLs (json and xml, in order): > > > > http://www.mysparlendpoint.com:8890/sparql/?query=%0Aprefix%20obo%3A%20%3Chttp%3A//purl.org/obo/owl/GO%23%3E%0Aprefix%20goformat%3A%20%3Chttp%3A//www.geneontology.org/formats/oboInOwl%23%3E%0Aprefix%20rdfs%3A%20%3Chttp%3A//www.w3.org/2000/01/rdf-schema%23%3E%0Aselect%20%3FmainName%0AFROM%20%3Chttp%3A//goOneProcess.com%3E%0Awhere%20{%0Aobo%3AGO_0006554%0Ardfs%3Alabel%20%3FmainName.%0A}&format=xml > > http://www.mysparlendpoint.com:8890/sparql/?query=%0Aprefix%20obo%3A%20%3Chttp%3A//purl.org/obo/owl/GO%23%3E%0Aprefix%20goformat%3A%20%3Chttp%3A//www.geneontology.org/formats/oboInOwl%23%3E%0Aprefix%20rdfs%3A%20%3Chttp%3A//www.w3.org/2000/01/rdf-schema%23%3E%0Aselect%20%3FmainName%0AFROM%20%3Chttp%3A//goOneProcess.com%3E%0Awhere%20{%0Aobo%3AGO_0006554%0Ardfs%3Alabel%20%3FmainName.%0A}&format=json > > > > In the json case, the error: > > { "head": { "link": [], "vars": ["mainName"] }, > > "results": { "distinct": false, "ordered": true, "bindings": [ > > { "mainName": { "type": "literal", "xml:lang": "22023 Error SR460: > > Function http_escape needs a varbinary or varchar argument 1 with length > > more than zero, not an arg of type DB_NULL (204) > > > > In the xml case: > > > > <?xml version="1.0" ?> > > > > <head> > > <variable name="mainName"/> > > </head> > > <results distinct="false" ordered="true"> > > <result>RDFXX Error Unknown language in DB.DBA.RDF_LANGUAGE_OF_LONG, bad > > id 258 > > > > > > > > > > > > <go0006554.rdf>------------------------------------------------------------------------------ > > This SF.net email is sponsored by: > > High Quality Requirements in a Collaborative Environment. > > Download a free trial of Rational Requirements Composer Now! > > http://p.sf.net/sfu/www-ibm-com_______________________________________________ > > Virtuoso-users mailing list > > Virtuoso-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/virtuoso-users > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com > _______________________________________________ Virtuoso-users mailing list > Virtuoso-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/virtuoso-users
