Hi Gohkan,
Per your suggestion, I added the Apply Construct module to the end of the
body. It's running faster overall, but I'm still seeing the slow down
behavior.
In addition, I've been trying different directories and the Convert XML to
RDF module is crashing (stack trace below) on one of the XML instance
files. Unfortunately I cannot tell which one even when running in Debug
mode. The file name is in a variable bound from the Iterate module but I
do not know how to make that display on the console as the script
executes. Since there are so many files, I don't really want to put in a
break point and manually step through until it crashes.
Is there a way to display the bound variables as the script executes?
Thanks,
Tim
java.lang.reflect.InvocationTargetException
at
org.topbraidcomposer.sparqlmotion.actions.AbstractExecuteSPARQLMotionAction$1.run(AbstractExecuteSPARQLMotionAction.java:148)
at org.topbraidcomposer.core.util.ThreadUtil$1$1.run(ThreadUtil.java:64)
at java.lang.Thread.run(Unknown Source)
Caused by: org.topbraid.spin.sparqlmotion.modules.SMException: Failed to
convert XML file using Semantic XML
at
org.topbraid.spin.sparqlmotion.lib.internal.ConvertXMLToRDFModule.createGraph(ConvertXMLToRDFModule.java:53)
at
org.topbraid.spin.sparqlmotion.modules.AbstractSMModule.getRDFOutput(AbstractSMModule.java:849)
at
org.topbraid.spin.sparqlmotion.engine.impl.ExecutionEngineImpl.executeModule(ExecutionEngineImpl.java:175)
at
org.topbraid.spin.sparqlmotion.engine.impl.ExecutionEngineImpl.execute(ExecutionEngineImpl.java:120)
at
org.topbraid.spin.sparqlmotion.modules.AbstractSMModule.executeSubScript(AbstractSMModule.java:292)
at
org.topbraid.spin.sparqlmotion.lib.internal.IterateOverSelectModule.access$0(IterateOverSelectModule.java:1)
at
org.topbraid.spin.sparqlmotion.lib.internal.IterateOverSelectModule$1.run(IterateOverSelectModule.java:175)
... 1 more
Caused by: java.util.ConcurrentModificationException
at
com.hp.hpl.jena.mem.HashCommon$BasicKeyIterator.hasNext(HashCommon.java:338)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:87)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:64)
at
com.hp.hpl.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:43)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:64)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:86)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:64)
at
com.hp.hpl.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:43)
at
com.hp.hpl.jena.graph.compose.CompositionBase$2.hasNext(CompositionBase.java:99)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:86)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:64)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:86)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:64)
at
com.hp.hpl.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:43)
at
com.hp.hpl.jena.graph.compose.CompositionBase$2.hasNext(CompositionBase.java:99)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:86)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:64)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:86)
at
com.hp.hpl.jena.graph.query.SimpleQueryHandler.subjectsFor(SimpleQueryHandler.java:61)
at
com.hp.hpl.jena.graph.query.SimpleQueryHandler.subjectsFor(SimpleQueryHandler.java:44)
at
com.hp.hpl.jena.rdf.model.impl.ModelCom.listSubjectsFor(ModelCom.java:1019)
at
com.hp.hpl.jena.rdf.model.impl.ModelCom.listResourcesWithProperty(ModelCom.java:1033)
at
com.hp.hpl.jena.rdf.model.impl.ModelCom.listSubjectsWithProperty(ModelCom.java:433)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.getExistingURISubject(XML2RDF.java:593)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.getExistingURISubject(XML2RDF.java:588)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.getAnnotatedElementClass(XML2RDF.java:351)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.getElementType(XML2RDF.java:504)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:141)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:126)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:236)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:126)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:236)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:126)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:236)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:126)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:236)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:126)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:236)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createElement(XML2RDF.java:126)
at
org.topbraid.spin.sparqlmotion.lib.internal.sxml.XML2RDF.createDocument(XML2RDF.java:119)
at org.topbraid.sxml.mapping.XML2RDFLoader.load(XML2RDFLoader.java:77)
at
org.topbraid.sparqlmotion.lib.convertXMLToRDF.ConvertXMLToRDFModule.load(ConvertXMLToRDFModule.java:24)
at
org.topbraid.spin.sparqlmotion.lib.internal.ConvertXMLToRDFModule.createGraph(ConvertXMLToRDFModule.java:50)
... 7 more
On Fri, Mar 16, 2012 at 3:44 PM, Tim Smith <[email protected]> wrote:
> One small correction - I'm using an Iterate Over Select module, not Bind
> by Select to process each file.
>
> Thanks,
>
> Tim
>
>
>
> On Fri, Mar 16, 2012 at 3:35 PM, Tim Smith <[email protected]> wrote:
>
>> Hi,
>>
>> I'm attempting to process ~250 XML files into RDF. I created a schema
>> for the files using XMLSpy and imported the schema into TBC using the XSD
>> importer. This created two .ttl files.
>>
>> I created an SM script that iterates over the files using tops:files via
>> a bind by select module. Prior to the Bind by Select, I import the schema
>> ontologies and my target ontology. In the body, I import each XML file,
>> convert it to RDF and then run a series of CONSTRUCT queries to map each
>> file into the target ontology. The combination of all triples generated is
>> then saved to disk.
>>
>> The script works fine if I only run through a small number of files.
>> However, if I try to hit all 250 at once, it just runs slower and slower
>> and slower... The slow part seems to be the CONSTRUCT queries. They run
>> fast initially but slow significantly after 10-20 files. For every file
>> that I have manually tested by running the CONSTRUCT query in the SPARQL
>> view, the query has always run very fast so I do not know why performance
>> is so poor running as an SM script.
>>
>> Any suggestions? Are there things I can do to speed this along? Is
>> there data that I can collect to better inform you?
>>
>> My current work around is to process each directory individually but even
>> that hits the problem because some directories have 10's of files (not to
>> mention the obvious hassle of changing the script - file names, base URIs,
>> etc... for each directory)
>>
>> I'm using 3.6B on win7/64 with 5G allocated to the JVM.
>>
>> Thanks,
>>
>> Tim
>>
>>
>
--
You received this message because you are subscribed to the Google
Group "TopBraid Suite Users", the topics of which include Enterprise Vocabulary
Network (EVN), TopBraid Composer,
TopBraid Live, TopBraid Ensemble, SPARQLMotion and SPIN.
To post to this group, send email to
[email protected]
To unsubscribe from this group, send email to
[email protected]
For more options, visit this group at
http://groups.google.com/group/topbraid-users?hl=en
