Hi Jerven, I have a copy of SPIN-API on GitHub that you can look at if you want to experiment with the new Jena/ARQ versions [1]. I am developing a SPIN plugin for the Bio2RDF webapp using it. I needed to make a few changes to SPIN-API to support function provenance and location mapping using custom OntModelSpec's, so it isn't a direct copy of SPIN-API 1.2.0 anymore, but I have tried to keep the majority of the original APIs as maps to the new functions.
If you want to experiment with the original SPIN-API 1.2.0 you can fork the repository and start a new branch from commit https://github.com/ansell/spin/commit/6380df8c7c4990809af2345d8432b78be3ab57b0 . Currently I am using the "sources" branch, as the "master" branch contains the first failed experiment. Currently SPIN-API 1.2.0 uses Jena-2.6.4 and ARQ 2.8.7. They broke the API in ARQ 2.8.8 ( even though it was named as a very minor release), but you could attempt to make it work with the current snapshots and skip 2.8.8. Cheers, Peter [1] http://github.com/ansell/spin On 16 November 2011 18:29, Jerven Bolleman <[email protected]> wrote: > Hi Holger, > > There are currently five patches attached to the JENA issue. Is this the > patch that you tested JENA-120-r1173178.patch? > > Or as an other option would you like me to test the jena-arq 2.8.9 SNAPSHOTS > and jena 2.6.5 SNAPSHOT? If this could be interesting for you its fine by me > as we are still in prototype stage. > > Regards, > Jerven > > On 11/15/2011 09:42 PM, Holger Knublauch wrote: >> >> Hi Jerven, >> >> this is a Jena/ARQ bug, see >> >> >> http://mail-archives.apache.org/mod_mbox/incubator-jena-users/201109.mbox/%[email protected]%3E >> >> The mail above contains a link to a simple patch to ARQ that will fix it. >> Let me know if you have trouble applying the patch. >> >> Regards >> Holger >> >> >> >> On Nov 16, 2011, at 1:34 AM, Jerven Bolleman wrote: >> >>> Hi Holger, All, >>> >>> I am getting the following exception when using two threads to run >>> SPINConstraints.check() on different ontmodels. >>> As on the same data/code this exception happens on different places I am >>> worried about thread safety. Should the spin API be threadsafe for this >>> operation? I did not see any note in the javadoc of SPINConstraints [1]. >>> >>> If yes I will need to work on getting a test case out to the ARQ >>> developers. >>> >>> Thanks and regards, >>> Jerven >>> >>> [1] >>> http://topbraid.org/spin/api/1.2.0/spin/apidocs/org/topbraid/spin/constraints/SPINConstraints.html >>> >>> 2011-11-15 13:04:31 +0000 org.expasy.rules.runners.ManyRuleRunner >>> ERROR: Exception >>> com.hp.hpl.jena.sparql.ARQInternalErrorException: Null for accumulator >>> at >>> com.hp.hpl.jena.sparql.expr.aggregate.AggregatorBase.getValue(AggregatorBase.java:61) >>> at >>> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup.calc(QueryIterGroup.java:121) >>> at >>> com.hp.hpl.jena.sparql.engine.iterator.QueryIterGroup.<init>(QueryIterGroup.java:32) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:413) >>> at >>> com.hp.hpl.jena.sparql.engine.main.ExecutionDispatch.visit(ExecutionDispatch.java:255) >>> at >>> com.hp.hpl.jena.sparql.algebra.op.OpGroup.visit(OpGroup.java:37) >>> at >>> com.hp.hpl.jena.sparql.engine.main.ExecutionDispatch.exec(ExecutionDispatch.java:33) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.executeOp(OpExecutor.java:107) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:272) >>> at >>> com.hp.hpl.jena.sparql.engine.main.ExecutionDispatch.visit(ExecutionDispatch.java:143) >>> at >>> com.hp.hpl.jena.sparql.algebra.op.OpFilter.visit(OpFilter.java:96) >>> at >>> com.hp.hpl.jena.sparql.engine.main.ExecutionDispatch.exec(ExecutionDispatch.java:33) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.executeOp(OpExecutor.java:107) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:196) >>> at >>> com.hp.hpl.jena.sparql.engine.main.ExecutionDispatch.visit(ExecutionDispatch.java:93) >>> at >>> com.hp.hpl.jena.sparql.algebra.op.OpSequence.visit(OpSequence.java:61) >>> at >>> com.hp.hpl.jena.sparql.engine.main.ExecutionDispatch.exec(ExecutionDispatch.java:33) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.executeOp(OpExecutor.java:107) >>> at >>> com.hp.hpl.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:80) >>> at com.hp.hpl.jena.sparql.engine.main.QC.execute(QC.java:40) >>> at >>> com.hp.hpl.jena.sparql.engine.main.QueryEngineMain.eval(QueryEngineMain.java:52) >>> at >>> com.hp.hpl.jena.sparql.engine.QueryEngineBase.evaluate(QueryEngineBase.java:138) >>> at >>> com.hp.hpl.jena.sparql.engine.QueryEngineBase.createPlan(QueryEngineBase.java:109) >>> at >>> com.hp.hpl.jena.sparql.engine.QueryEngineBase.getPlan(QueryEngineBase.java:97) >>> at >>> com.hp.hpl.jena.sparql.engine.main.QueryEngineMain$1.create(QueryEngineMain.java:91) >>> at >>> com.hp.hpl.jena.sparql.engine.QueryExecutionBase.getPlan(QueryExecutionBase.java:266) >>> at >>> com.hp.hpl.jena.sparql.engine.QueryExecutionBase.startQueryIterator(QueryExecutionBase.java:243) >>> at >>> com.hp.hpl.jena.sparql.engine.QueryExecutionBase.execConstruct(QueryExecutionBase.java:110) >>> at >>> org.topbraid.spin.constraints.SPINConstraints.runQueryOnClass(SPINConstraints.java:491) >>> at >>> org.topbraid.spin.constraints.SPINConstraints.run(SPINConstraints.java:458) >>> at >>> org.topbraid.spin.constraints.SPINConstraints.check(SPINConstraints.java:313) >>> at >>> org.expasy.rules.runners.ManyRuleRunner.runRules(ManyRuleRunner.java:123) >>> at >>> org.expasy.rules.runners.ManyRuleRunner$SparqlRuleRunner.runRules(ManyRuleRunner.java:271) >>> at >>> org.expasy.rules.runners.ManyRuleRunner$RuleRunner.run(ManyRuleRunner.java:313) >>> at >>> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) >>> at >>> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) >>> at java.util.concurrent.FutureTask.run(FutureTask.java:138) >>> at >>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) >>> at >>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) >>> at java.lang.Thread.run(Thread.java:662) >>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Group "TopBraid Suite Users", the topics of which include 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 >> > > > -- > ------------------------------------------------------------------- > Jerven Bolleman [email protected] > Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85 > CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58 > 1211 Geneve 4, > Switzerland www.isb-sib.ch - www.uniprot.org > Follow us at https://twitter.com/#!/uniprot > ------------------------------------------------------------------- > > -- > You received this message because you are subscribed to the Google > Group "TopBraid Suite Users", the topics of which include 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 > -- You received this message because you are subscribed to the Google Group "TopBraid Suite Users", the topics of which include TopBraid Composer, TopBraid Live, TopBraid Ensemble, SPARQLMotion and SPIN. 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