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Posted to users@jena.apache.org by Brad Stallion <br...@yahoo.com.INVALID> on 2018/11/29 15:07:08 UTC
Problems clearing/deleting TDB
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
Re: Problems clearing/deleting TDB
Posted by Andy Seaborne <an...@apache.org>.
Recorded as JENA-1643
On 29/11/2018 18:58, Andy Seaborne wrote:
> Brad,
>
> Thanks for the report. Could you raise a JIRA ticket please? It's a bug.
> The BaseInfGraph.clear should be inside a transaction and somehow that's
> getting missed.
>
> Other updates work (e.g. insert data) so it's specific to "clear"
> somehow. It was supposed to be fixed at JENA-1492 which is 3.7.0.
>
> Andy
>
> On 29/11/2018 15:07, Brad Stallion wrote:
>> 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
>>
Re: Problems clearing/deleting TDB
Posted by Andy Seaborne <an...@apache.org>.
Brad,
Thanks for the report. Could you raise a JIRA ticket please? It's a bug.
The BaseInfGraph.clear should be inside a transaction and somehow that's
getting missed.
Other updates work (e.g. insert data) so it's specific to "clear"
somehow. It was supposed to be fixed at JENA-1492 which is 3.7.0.
Andy
On 29/11/2018 15:07, Brad Stallion wrote:
> 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
>
Re: Problems clearing/deleting TDB
Posted by Brad Stallion <br...@yahoo.com.INVALID>.
Thanks a lot Andy! It works!!!
Il venerdì 30 novembre 2018, 11:14:38 CET, Andy Seaborne <an...@apache.org> ha scritto:
On 30/11/2018 08:56, Brad Stallion wrote:
> Hi, thanks for your reply.DROP ALL returns "500 Read-only block manager"
> If I try on of:
> DROP GRAPH <#model2>DROP GRAPH <#tdbGraph>DROP GRAPH <#dataset2>
> no error is thrown but nothing change -- no triple is deleted.Any idea?Thanks
The graph is the default graph of the dataset, not a named graph. DROP
or CLEAR on a non-existent graph does not cause any updates to be
attempted so does not go near the database.
Workaround:
Fot eh CLEAR do a multiple operation SPARQL Update:
Delete a non-existent triple (or an existing one) then do the clear.
DELETE DATA { <ex:s> a <ex:T> } ; CLEAR ALL
The DELETE DATA will put the operation into write mode.
See other email in this conversation, timestamp: Thu, 29 Nov 2018
18:58:50 +0000
Andy
>
> Il giovedì 29 novembre 2018, 18:20:06 CET, ajs6f <aj...@apache.org> ha scritto:
>
> I can't speak precisely to your error, but have you tried DROP GRAPH [1]? Might be a useful workaround for the moment.
>
> ajs6f
>
> [1] https://www.w3.org/TR/sparql11-update/#drop
>
>> On Nov 29, 2018, at 10:07 AM, Brad Stallion <br...@yahoo.com.INVALID> wrote:
>>
>> 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
>>
>> <config.ttl>
>
>
Re: Problems clearing/deleting TDB
Posted by Andy Seaborne <an...@apache.org>.
On 30/11/2018 08:56, Brad Stallion wrote:
> Hi, thanks for your reply.DROP ALL returns "500 Read-only block manager"
> If I try on of:
> DROP GRAPH <#model2>DROP GRAPH <#tdbGraph>DROP GRAPH <#dataset2>
> no error is thrown but nothing change -- no triple is deleted.Any idea?Thanks
The graph is the default graph of the dataset, not a named graph. DROP
or CLEAR on a non-existent graph does not cause any updates to be
attempted so does not go near the database.
Workaround:
Fot eh CLEAR do a multiple operation SPARQL Update:
Delete a non-existent triple (or an existing one) then do the clear.
DELETE DATA { <ex:s> a <ex:T> } ; CLEAR ALL
The DELETE DATA will put the operation into write mode.
See other email in this conversation, timestamp: Thu, 29 Nov 2018
18:58:50 +0000
Andy
>
> Il giovedì 29 novembre 2018, 18:20:06 CET, ajs6f <aj...@apache.org> ha scritto:
>
> I can't speak precisely to your error, but have you tried DROP GRAPH [1]? Might be a useful workaround for the moment.
>
> ajs6f
>
> [1] https://www.w3.org/TR/sparql11-update/#drop
>
>> On Nov 29, 2018, at 10:07 AM, Brad Stallion <br...@yahoo.com.INVALID> wrote:
>>
>> 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
>>
>> <config.ttl>
>
>
Re: Problems clearing/deleting TDB
Posted by Brad Stallion <br...@yahoo.com.INVALID>.
Hi, thanks for your reply.DROP ALL returns "500 Read-only block manager"
If I try on of:
DROP GRAPH <#model2>DROP GRAPH <#tdbGraph>DROP GRAPH <#dataset2>
no error is thrown but nothing change -- no triple is deleted.Any idea?Thanks
Il giovedì 29 novembre 2018, 18:20:06 CET, ajs6f <aj...@apache.org> ha scritto:
I can't speak precisely to your error, but have you tried DROP GRAPH [1]? Might be a useful workaround for the moment.
ajs6f
[1] https://www.w3.org/TR/sparql11-update/#drop
> On Nov 29, 2018, at 10:07 AM, Brad Stallion <br...@yahoo.com.INVALID> wrote:
>
> 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
>
> <config.ttl>
Re: Problems clearing/deleting TDB
Posted by ajs6f <aj...@apache.org>.
I can't speak precisely to your error, but have you tried DROP GRAPH [1]? Might be a useful workaround for the moment.
ajs6f
[1] https://www.w3.org/TR/sparql11-update/#drop
> On Nov 29, 2018, at 10:07 AM, Brad Stallion <br...@yahoo.com.INVALID> wrote:
>
> 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
>
> <config.ttl>