Marco, While I trying to reproduce the original loading/corruption problem, you may INSERT INTO DB.DBA.RDF_LANGUAGE (RL_ID, RL_TWOBYTE) values (258, 'en'); SHUTDOWN; and start the server again. We knows from sample data and from error message that 258 should correspond to 'en', so this dirty hack may let you either work with existing database or get next error to study. (if next error is of same sort then maybe it can be fixed same way).
The trick may fail if the server was restarted after the failed load AND more data were loaded after that. In this case you'll get "uniqueness violation error". In that case you may cheat one more time and try, say, INSERT INTO DB.DBA.RDF_LANGUAGE (RL_ID, RL_TWOBYTE) values (258, 'en-US'); in hope that the difference between 'en' and 'en-US' will be less critical than data unavailability. Best Regards, Ivan Mikhailov, OpenLink Software http://virtuoso.openlinksw.com On Thu, 2009-04-09 at 19:20 -0700, Marco Ocana wrote: > 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 > > > ------------------------------------------------------------------------------ > 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
