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Re: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph()
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From: Rob N. <ro...@co...> - 2014-02-06 16:32:32
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Thanks for your help Rob, Yes pretty much where we got to. Its totally sporadic, and hard to reproduce. It works sometimes, and not others it either always works, or always stackoverflows, on multiple environments (irrelevant of build settings). We first used a named graph, and now we dont. Left the queries (several hundred of them) using named graphs as doesnt (seem to, were still learning) make any difference as you mention. dotNetRDF > pulled via nuget Version: 1.0.3.0 Description: API for manipulating RDF data (.Net 4.0) Based on it probably being a environment or config related issue, and before you waste any more time, Ill try some more debugging off your code base (rather than release assemblies) and double checking our dependency graph to make its not something else impacting. The triple store is over a gigabyte I believe, so will try and avoid sending that over for the time being. Many thanks. From: Rob Vesse [mailto:rv...@do...] Sent: 06 February 2014 15:16 To: dotNetRDF Developer Discussion and Feature Request Cc: Rob Nicholls Subject: Re: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() So I am pretty stumped on this as I've been completely unable to reproduce this after several hours of trying. I checked whether you could easily hit a StackOverflow with the RDF/XML parser and you really can't. I wrote unit tests which call the parser from 5,000 levels deep of recursion and did not get a StackOverflow so I don't see how the data alone could cause the issue. I've also put the data you provided into a local instance of Fuseki and ran the query against it using SparqlRemoteEndpoint.QueryWithResultGraph() and I cannot produce a StackOverflow. Part of my problem is that I just don't seem to have quite the same setup as you, your query uses named graphs but your data does not include them so I had to modify the query slightly. Yet I don't see how that would make any difference especially since the CONSTRUCT template remains identical between your query and mine so the data received should be identical. You state that you've reproduced this in a console app so could you please provide your console app that reproduces the issue along with your raw data (assuming a TDB database zipping up the TDB folder would provide this) that I can run under the debugger on my system to see what is going on? Failing that can you run under the debugger and capture what the stack trace is at the point where the StackOverflowException gets thrown? As otherwise I can't really do any further useful debugging on this. Also can you please confirm again exactly the build of dotNetRDF being used? If you can look at the properties for the dotNetRDF dependency in VS and look at the Version and the Description strings and provide that information, the Description is particularly relevant because that will tell me exactly which of the core library builds you are using. Thanks, Rob From: Rob Vesse <rv...@do...> Reply-To: dotNetRDF Developer Discussion and Feature Request <dot...@li...> Date: Thursday, 6 February 2014 11:12 To: Rob Nicholls <ro...@co...> Cc: dotNetRDF Developer Discussion and Feature Request <dot...@li...> Subject: SPAM-LOW: Re: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() Thanks for the additional information, the RDF/XML is perfectly valid as you noted. That error is not really more descriptive, turning on the HTTP Full Debugging consumes the response stream so the calling code then has an already closed stream which causes different errors depending on the calling code. I've changed this behaviour in our default branch so that it'll now throw an error informing you that the response stream was consumed and not available to calling code. The RDF/XML parser code does recurse heavily so I'm wondering if this file is just under the stack limit when parsed in the rdfEditor but when called via the SparqlRemoteEndpoint which itself has several levels of recursion tips it over the edge. I'm going to take the data you provided and debug this further and will get back to you when I know more Rob From: Rob Nicholls <ro...@co...> Date: Monday, 3 February 2014 13:46 To: Rob Vesse <rv...@do...> Cc: 'dotNetRDF Developer Discussion and Feature Request' <dot...@li...> Subject: RE: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() Ahh, missed that. Thanks. Ok, now throwing a more descriptive error; XML parser, root element is missing. Output attached. Ive checked the RDF with your RDFeditor validator, no problems. Is it feasibly a memory issue, based on the size of the RDF/XML? (Ive stripped the code right back to a simple console app using dotNetRDF same result) Or maybe Im missing something obvious? /Rob From: Rob Vesse [mailto:rv...@do...] Sent: 30 January 2014 19:16 To: Rob Nicholls Cc: dotNetRDF Developer Discussion and Feature Request Subject: Re: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() Ok, that's useful information. Specific version of Fuseki should not be an issue since I don't see anything in the query that would trigger any known bugs in Fuseki/TDB/ARQ Would be interesting to see what format Fuseki is returning the data in when called from dotNetRDF. Could you run the query with HTTP Debugging turned on as detailed at [1] and provide the HTTP traces this produces to the console? The full HTTP trace could be particularly useful in determining if there is something in the data serialisation of the results of this query that triggers a SO in one of the dotNetRDF parsers. Thanks, Rob [1]: https://bitbucket.org/dotnetrdf/dotnetrdf/wiki/HowTo/Debug%20HTTP%20Communic ation.wiki#!debugging-http-communication From: Rob Nicholls <ro...@co...> Date: Thursday, 30 January 2014 10:26 To: Rob Vesse <rv...@do...>, 'dotNetRDF Developer Discussion and Feature Request' <dot...@li...> Subject: RE: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() dotnetRDF library to query (via .NET4.5 build) Jena Fuseki for the Triple Store and Endpoint (I forget specific versions, but will check if helpful) mmx is our Dataset Calling code is basically (omitted the noise): _endpoint = new SparqlRemoteEndpoint(http://jena:3030/mmx/query); IGraph graph = _endpoint.QueryWithResultGraph(thequery); // ß Stackoverflow here Where thequery is: 1 PREFIX dc: <http://purl.org/dc/elements/1.1/> 2 PREFIX exif: <http://www.w3.org/2003/12/exif/ns/> 3 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema# <http://www.w3.org/2000/01/rdf-schema> > 4 PREFIX mmx: <http://data.sciencemuseum.org.uk/def/ontology/> 5 PREFIX foaf: <http://xmlns.com/foaf/0.1/> 6 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns# <http://www.w3.org/1999/02/22-rdf-syntax-ns> > 7 PREFIX skos: <http://www.w3.org/2004/02/skos/core# <http://www.w3.org/2004/02/skos/core> > 8 PREFIX dcterms: <http://purl.org/dc/terms/> 9 10 CONSTRUCT 11 { ?ass mmx:relatedArchiveDocument <http://id.sciencemuseum.org.uk/archivedocument/smad-110001337> . 12 ?ass rdf:type mmx:Asset . 13 ?ass dcterms:hasVersion ?ver . 14 ?ver ?pred2 ?obj2 . 15 ?ass ?p2 ?o2 .} 16 WHERE 17 { { GRAPH ?g 18 { ?ass mmx:relatedArchiveDocument <http://id.sciencemuseum.org.uk/archivedocument/smad-110001337> . 19 ?ass dcterms:hasVersion ?ver . 20 ?ver ?pred2 ?obj2 21 } 22 } 23 UNION 24 { GRAPH ?g 25 { ?ass mmx:relatedArchiveDocument <http://id.sciencemuseum.org.uk/archivedocument/smad-110001337> . 26 ?ass ?p2 ?o2 27 } 28 } 29 } Thought Id exclude the setup and query as, as mentioned, the query does work (and did, only recently started throwing the exception hence I wondered if it was data, or maybe encoding, related based on how dotnetRDF is parsing ). The attached triples were the result of the construct from above, not the entire triple store. This all works fine for small result sets, its just this particular query returns 360 relatedArchiveDocuments and the library doesnt seem to like it. If its nothing obvious, I will grab your source code and try and debug further cant tell much of what is happening within QueryWithResultGraph() atm. /Rob From: Rob Vesse [mailto:rv...@do...] Sent: 30 January 2014 17:12 To: dotNetRDF Developer Discussion and Feature Request Cc: ro...@co... Subject: Re: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() Rob You didn't include the query or any context of how you invoke the query so we can't really offer any attempt at diagnosis. Please provide a minimal complete example. Are the results you provided the results of a successful run of the specific query or a dump of the entire test dataset? Nothing looks untoward with the data so likely some interaction with the specific query. QueryWithResultGraph() implies use of SparqlRemoteEndpoint (whether directly/indirectly) to query a remote service so can you provide the code that invokes the query plus the specific problematic query. The only kind of query that springs to mind that could easily lead to a StackOverflow would be a complex property path but without seeing the query I can't tell, it may well be something innocuous hitting a rare corner case in our SPARQL engine. Also what can you tell us about the set up of that remote service since you imply you control that as well. Is the remote server using dotNetRDF to host the data, if so what's the setup? Or if it isn't under your control can you tell us anything about it e.g. endpoint, server software if known etc Thanks, Rob Vesse From: Rob Nicholls <ro...@co...> Reply-To: dotNetRDF Developer Discussion and Feature Request <dot...@li...> Date: Thursday, 30 January 2014 05:44 To: <dot...@li...> Subject: [dotNetRDF-Develop] Stackoverflow calling QueryWithResultGraph() Hi all, Im receiving consistent stack overflows from QueryWithResultGraph(query) when using a specific query against our triple store. The query runs fine (within ms) and returns results ok. Results returned from the triple store are in the attached file (queryresults.txt), not a huge amount of data to justify killing a 12GB web server, and it does occasionally function correctly on my developer machine (never when running the debugger though). Can anyone offer any advice? Is this perhaps an issue with the data itself causing some kind of circular reference? Although doesnt explain why it occasionally works. Using: dotnetRdf 1.0.3 / .NET4.5 Many thanks, Rob cogapp Rob Nicholls Senior Programmer +44 1273 821600 <http://www.cogapp.com/> www.cogapp.com Cogapp Brighton 21-33 Dyke Road, Brighton, BN1 3FE. UK Cogapp New York 641 Lexington Avenue, 15th Floor, New York, NY 10022, USA News Pocahontas' portrait and letters from George Washington online: a responsive website for the <http://www.vahistorical.org/> Virginia Historical Society, just launched. For regular Cogapp news, please follow us on <https://twitter.com/cogapp> Twitter. ---------------------------------------------------------------------------- -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. 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