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LinkedDataFragments / Server.Java

A Triple Pattern Fragments server for Java
MIT License
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TDB data source incompatible with new Jena #53

Open smalyshev opened 5 years ago

smalyshev commented 5 years ago

I tried to upgrade this package to Jena 3.10.0 (since 3.1.0 has dependencies which have some security issues) and I get Not in a transaction exceptions in tests, e.g.:

estEstimate(org.linkeddatafragments.test.datasource.JenaTDBDataSourceTest)  Time elapsed: 0.003 sec  <<< ERROR!
org.apache.jena.tdb.transaction.TDBTransactionException: Not in a transaction
    at org.apache.jena.tdb.transaction.DatasetGraphTransaction.get(DatasetGraphTransaction.java:140)
    at org.apache.jena.tdb.transaction.DatasetGraphTransaction.getDatasetGraphToQuery(DatasetGraphTransaction.java:86)
    at org.apache.jena.tdb.store.GraphTxnTDB.getDatasetGraphTDB(GraphTxnTDB.java:51)
    at org.apache.jena.tdb.store.GraphTDB.getNodeTupleTable(GraphTDB.java:89)
    at org.apache.jena.tdb.solver.SolverLib.execute(SolverLib.java:66)
    at org.apache.jena.tdb.solver.StageGeneratorDirectTDB.execute(StageGeneratorDirectTDB.java:56)
    at org.apache.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:128)
    at org.apache.jena.sparql.engine.main.ExecutionDispatch.visit(ExecutionDispatch.java:58)
    at org.apache.jena.sparql.algebra.op.OpBGP.visit(OpBGP.java:49)
    at org.apache.jena.sparql.engine.main.ExecutionDispatch.exec(ExecutionDispatch.java:46)
    at org.apache.jena.sparql.engine.main.OpExecutor.exec(OpExecutor.java:117)
    at org.apache.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:376)
    at org.apache.jena.sparql.engine.main.ExecutionDispatch.visit(ExecutionDispatch.java:323)
    at org.apache.jena.sparql.algebra.op.OpTopN.visit(OpTopN.java:50)
    at org.apache.jena.sparql.engine.main.ExecutionDispatch.exec(ExecutionDispatch.java:46)
    at org.apache.jena.sparql.engine.main.OpExecutor.exec(OpExecutor.java:117)
    at org.apache.jena.sparql.engine.main.OpExecutor.execute(OpExecutor.java:88)
    at org.apache.jena.sparql.engine.main.QC.execute(QC.java:52)
    at org.apache.jena.sparql.engine.main.QueryEngineMain.eval(QueryEngineMain.java:55)
    at org.apache.jena.sparql.engine.QueryEngineBase.evaluate(QueryEngineBase.java:175)
    at org.apache.jena.sparql.engine.QueryEngineBase.createPlan(QueryEngineBase.java:131)
    at org.apache.jena.sparql.engine.QueryEngineBase.getPlan(QueryEngineBase.java:112)
    at org.apache.jena.sparql.engine.main.QueryEngineMain$QueryEngineMainFactory.create(QueryEngineMain.java:90)
    at org.apache.jena.sparql.engine.QueryExecutionBase.getPlan(QueryExecutionBase.java:600)
    at org.apache.jena.sparql.engine.QueryExecutionBase.startQueryIterator(QueryExecutionBase.java:545)
    at org.apache.jena.sparql.engine.QueryExecutionBase.execConstructTriples(QueryExecutionBase.java:238)
    at org.apache.jena.sparql.engine.QueryExecutionBase.execConstruct(QueryExecutionBase.java:211)
    at org.linkeddatafragments.datasource.tdb.JenaTDBBasedRequestProcessorForTPFs$Worker.createFragment(JenaTDBBasedRequestProcessorForTPFs.java:116)
    at org.linkeddatafragments.datasource.AbstractRequestProcessorForTriplePatterns$Worker.createRequestedFragment(AbstractRequestProcessorForTriplePatterns.java:102)
    at org.linkeddatafragments.datasource.AbstractRequestProcessor.createRequestedFragment(AbstractRequestProcessor.java:29)
    at org.linkeddatafragments.test.datasource.DataSourceTest.testEstimate(DataSourceTest.java:151)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
    at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
    at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
    at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
    at org.junit.runners.Suite.runChild(Suite.java:127)
    at org.junit.runners.Suite.runChild(Suite.java:26)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
    at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
    at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
    at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
    at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
    at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
    at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
    at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)

Looks like something needs to be done to keep compatibility with latest Jena?

smalyshev commented 5 years ago

@mielvds maybe you know what's wrong there?

mielvds commented 5 years ago

Let me see. What did you change? Can you post the new pom.xml?

smalyshev commented 5 years ago

I set all Jena versions to 3.10.0. Also, I added dataset.begin(ReadWrite.WRITE); to JenaTDBDataSourceTest.java on line 63, otherwise it threw "Not in a transaction" there. You can see our full pom.xml here: https://gist.github.com/smalyshev/b8045f8e15f0c926df003f67ecbaf492 - it's a bit different from master since we did other fixes but close enough. I think you'd be able to see it just replacing all Jena component versions to 3.10.0 and running mvn install.

mielvds commented 5 years ago

No idea really, maybe @barthanssens can answer this?

barthanssens commented 5 years ago

I'm mainly working with RDF4J, so I'm guessing here based on some quick googling :-)

It appears to be that there were changes in Jena, and things like qexec.execConstruct(triples); (line 116) seems to be valid only in a transaction...

If you prefer some syntactic sugar, there is also a convenience library ´Txn´ for handling transactions in a lambda expression: http://jena.apache.org/documentation/txn/txn.html