Brad Stallion
2018-11-29 15:07:08 UTC
Hi All,I'm using Fuseki 3.9.0. I have a TDB-backed graph. Configuration file is attached.Everything works, including inference on triples added incrementally.I'd like to reset the TDB content.
The SPARQL directive "DELETE { ?s ?p ?o } WHERE { ?s ?p ?o }" is too slow.
The directive "CLEAR ALL", once I've put something in the TDB, gives the following error:
org.apache.jena.tdb.TDBException: Read-only block manager at org.apache.jena.tdb.base.block.BlockMgrReadonly.beginUpdate(BlockMgrReadonly.java:33) at org.apache.jena.tdb.base.page.PageBlockMgr.startUpdate(PageBlockMgr.java:131) at org.apache.jena.tdb.index.bplustree.BPlusTree.startUpdateBlkMgr(BPlusTree.java:404) at org.apache.jena.tdb.index.bplustree.BPlusTree.deleteAndReturnOld(BPlusTree.java:339) at org.apache.jena.tdb.index.bplustree.BPlusTree.delete(BPlusTree.java:335) at org.apache.jena.tdb.store.tupletable.TupleIndexRecord.performDelete(TupleIndexRecord.java:69) at org.apache.jena.tdb.store.tupletable.TupleIndexBase.delete(TupleIndexBase.java:74) at org.apache.jena.tdb.store.tupletable.TupleTable.delete(TupleTable.java:148) at org.apache.jena.tdb.store.DatasetGraphTDB.deleteAny(DatasetGraphTDB.java:239) at org.apache.jena.tdb.store.GraphTDB.clear(GraphTDB.java:174) at org.apache.jena.reasoner.BaseInfGraph.clear(BaseInfGraph.java:155) at org.apache.jena.sparql.modify.UpdateEngineWorker.execDropClear(UpdateEngineWorker.java:107) at org.apache.jena.sparql.modify.UpdateEngineWorker.execDropClear(UpdateEngineWorker.java:87) at org.apache.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:83) at org.apache.jena.sparql.modify.request.UpdateClear.visit(UpdateClear.java:35) at org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:46) at org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:26) at org.apache.jena.atlas.iterator.Iter.sendToSink(Iter.java:562) at org.apache.jena.atlas.iterator.Iter.sendToSink(Iter.java:569) at org.apache.jena.sparql.modify.UpdateProcessorBase.execute(UpdateProcessorBase.java:59) at org.apache.jena.update.UpdateAction.execute$(UpdateAction.java:228) at org.apache.jena.update.UpdateAction.execute(UpdateAction.java:194) at org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:235) at org.apache.jena.fuseki.servlets.SPARQL_Update.executeForm(SPARQL_Update.java:204) at org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:109) at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:183) at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:98) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:74) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642) at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642) at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285) at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1634) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1340) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1242) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144) at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:690) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.Server.handle(Server.java:503) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:364) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:260) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:118) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:126) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:366) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:765) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:683) at java.lang.Thread.run(Thread.java:745)[2018-11-29 16:03:01] Fuseki   INFO [6259] 500 Read-only block manager (5 ms)
If I try to delete the dataset by using the "remove" button on web interface I get:
Sorry, removing dataset /pluto did not work, because: 'There are 6262 configuration files, not one. Delete not performed; clearup of the filesystem needed.'
Anyway, I'd like to have "CLEAR ALL" command working: any idea?
Thanks
The SPARQL directive "DELETE { ?s ?p ?o } WHERE { ?s ?p ?o }" is too slow.
The directive "CLEAR ALL", once I've put something in the TDB, gives the following error:
org.apache.jena.tdb.TDBException: Read-only block manager at org.apache.jena.tdb.base.block.BlockMgrReadonly.beginUpdate(BlockMgrReadonly.java:33) at org.apache.jena.tdb.base.page.PageBlockMgr.startUpdate(PageBlockMgr.java:131) at org.apache.jena.tdb.index.bplustree.BPlusTree.startUpdateBlkMgr(BPlusTree.java:404) at org.apache.jena.tdb.index.bplustree.BPlusTree.deleteAndReturnOld(BPlusTree.java:339) at org.apache.jena.tdb.index.bplustree.BPlusTree.delete(BPlusTree.java:335) at org.apache.jena.tdb.store.tupletable.TupleIndexRecord.performDelete(TupleIndexRecord.java:69) at org.apache.jena.tdb.store.tupletable.TupleIndexBase.delete(TupleIndexBase.java:74) at org.apache.jena.tdb.store.tupletable.TupleTable.delete(TupleTable.java:148) at org.apache.jena.tdb.store.DatasetGraphTDB.deleteAny(DatasetGraphTDB.java:239) at org.apache.jena.tdb.store.GraphTDB.clear(GraphTDB.java:174) at org.apache.jena.reasoner.BaseInfGraph.clear(BaseInfGraph.java:155) at org.apache.jena.sparql.modify.UpdateEngineWorker.execDropClear(UpdateEngineWorker.java:107) at org.apache.jena.sparql.modify.UpdateEngineWorker.execDropClear(UpdateEngineWorker.java:87) at org.apache.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:83) at org.apache.jena.sparql.modify.request.UpdateClear.visit(UpdateClear.java:35) at org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:46) at org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:26) at org.apache.jena.atlas.iterator.Iter.sendToSink(Iter.java:562) at org.apache.jena.atlas.iterator.Iter.sendToSink(Iter.java:569) at org.apache.jena.sparql.modify.UpdateProcessorBase.execute(UpdateProcessorBase.java:59) at org.apache.jena.update.UpdateAction.execute$(UpdateAction.java:228) at org.apache.jena.update.UpdateAction.execute(UpdateAction.java:194) at org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:235) at org.apache.jena.fuseki.servlets.SPARQL_Update.executeForm(SPARQL_Update.java:204) at org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:109) at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:183) at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:98) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:74) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642) at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642) at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285) at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1634) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1340) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1242) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144) at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:690) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.Server.handle(Server.java:503) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:364) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:260) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:118) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:126) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:366) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:765) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:683) at java.lang.Thread.run(Thread.java:745)[2018-11-29 16:03:01] Fuseki   INFO [6259] 500 Read-only block manager (5 ms)
If I try to delete the dataset by using the "remove" button on web interface I get:
Sorry, removing dataset /pluto did not work, because: 'There are 6262 configuration files, not one. Delete not performed; clearup of the filesystem needed.'
Anyway, I'd like to have "CLEAR ALL" command working: any idea?
Thanks