Tim,
You may want to try assigning different sml:baseURI values in the
sml:ConvertXMLToRDF for each iteration.
Gokhan
On 3/16/2012 2:10 PM, Tim Smith wrote:
More investigation into the Convert XML to RDF module crashing.
This only seems to occur when running multiple threads. As long as I
only use one thread it will process the files correctly, albeit slowly.
I guess this is one of the watchouts for using multiple threads!
Tim
On Fri, Mar 16, 2012 at 4:31 PM, Tim Smith <[email protected]
<mailto:[email protected]>> wrote:
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]
<mailto:[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] <mailto:[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
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