Develop Reference

How do deal with h2 databases inability to deal with interrupts

How do deal with h2 database inability to deal with interrupts, I was occasionally seeing that my embedded h2 database appeared to get corrupted, in particular I had amended an ExecutorService so that if a task took too long it would cancel the task. The task would be cancelled okay but then subsequent database access failed with exceptions such as
23/07/2019 14.23.31:BST:DeleteDuplicatesController:start:SEVERE: commit failed
org.hibernate.TransactionException: commit failed
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:187)
at com.jthink.songkong.db.ReportCache.save(ReportCache.java:46)
at com.jthink.songkong.reports.AbstractReport.setReportDatabaseObject(AbstractReport.java:365)
at com.jthink.songkong.reports.DeleteDuplicatesReport.setReportDatabaseObject(DeleteDuplicatesReport.java:333)
at com.jthink.songkong.reports.DeleteDuplicatesReport.closeReport(DeleteDuplicatesReport.java:377)
at com.jthink.songkong.analyse.toplevelanalyzer.DeleteDuplicatesController.deleteAnyDups(DeleteDuplicatesController.java:606)
at com.jthink.songkong.analyse.toplevelanalyzer.DeleteDuplicatesController.start(DeleteDuplicatesController.java:665)
at com.jthink.songkong.ui.swingworker.DeleteDuplicates.doInBackground(DeleteDuplicates.java:43)
at com.jthink.songkong.ui.swingworker.DeleteDuplicates.doInBackground(DeleteDuplicates.java:20)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.hibernate.TransactionException: unable to commit against JDBC connection
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doCommit(JdbcTransaction.java:116)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:180)
... 14 more
Caused by: org.h2.jdbc.JdbcSQLNonTransientException: General error: "java.lang.IllegalStateException: Reading from nio:C:/Users/Paul/AppData/Roaming/SongKong/Database/Database.mv.db failed; file length -1 read length 4096 at 1541494 [1.4.199/1]"; SQL statement:
COMMIT [50000-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:502)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427)
at org.h2.message.DbException.get(DbException.java:194)
at org.h2.message.DbException.convert(DbException.java:347)
at org.h2.command.Command.executeUpdate(Command.java:280)
at org.h2.jdbc.JdbcConnection.commit(JdbcConnection.java:542)
at com.mchange.v2.c3p0.impl.NewProxyConnection.commit(NewProxyConnection.java:1284)
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doCommit(JdbcTransaction.java:112)
... 15 more
Caused by: java.lang.IllegalStateException: Reading from nio:C:/Users/Paul/AppData/Roaming/SongKong/Database/Database.mv.db failed; file length -1 read length 4096 at 1541494 [1.4.199/1]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:883)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:420)
at org.h2.mvstore.FileStore.readFully(FileStore.java:98)
at org.h2.mvstore.MVStore.readBufferForPage(MVStore.java:1048)
at org.h2.mvstore.MVStore.readPage(MVStore.java:2186)
at org.h2.mvstore.MVMap.readPage(MVMap.java:554)
at org.h2.mvstore.Page$NonLeaf.getChildPage(Page.java:1086)
at org.h2.mvstore.Page.get(Page.java:221)
at org.h2.mvstore.MVMap.get(MVMap.java:402)
at org.h2.mvstore.MVMap.get(MVMap.java:389)
at org.h2.mvstore.MVStore.getMapName(MVStore.java:2737)
at org.h2.mvstore.MVStore.renameMap(MVStore.java:2650)
at org.h2.mvstore.tx.TransactionStore.commit(TransactionStore.java:453)
at org.h2.mvstore.tx.Transaction.commit(Transaction.java:389)
at org.h2.engine.Session.commit(Session.java:691)
at org.h2.command.dml.TransactionCommand.update(TransactionCommand.java:46)
at org.h2.command.CommandContainer.update(CommandContainer.java:133)
at org.h2.command.Command.executeUpdate(Command.java:267)
... 18 more
Caused by: java.nio.channels.ClosedChannelException
at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:721)
at org.h2.store.fs.FileNio.read(FilePathNio.java:74)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:406)
... 34 more
23/07/2019 14.23.31:BST:Errors:addError:SEVERE: Adding Error:commit failed
I have since found this issue
Basically if using H2 in embedded mode, and it receives an interrupt then all subsequent access fails until the thread pool is close and reopened. In the example I give of a process having to be cancelled because it appears to be stuck there is no solution except for interrupting
I also have another case whereby usually the controller thread that doesn't directly do a database work itself so I was struggling to see why when an interrupt occurred why this would cause database errors since this is handled by controller thread. I have now worked out the issue is that Im using an ExecutorService with a fixed size BlockingQueue (so that we dont have a big queue build up in memory), but if the queue gets full then new task is actually executed by the controller thread (because of CallerRunsPolicy), so the controller thread can be making calls to database after all.
Im using H2 with hibernate and in both cases calling the following immediately after the interrupt
HibernateUtil.closeFactory();
seems to solve the issue, however I guess this means that any other threads with hibernate sessions will be broken, but at least newly opened sessins will be okay. So im not particularly happy with this workaround, any other ideas ?
Using H2 as a server is not a solution since the whole point of H2 was an embedded db self contained within application.

Although not properly documented using the async protocol allows a connection to be interrupted without breaking all other connections.

Phoenix hbase java.util.concurrent.CancellationException error

I have used batch process to execute some opration on hbase table using phoenix every 2 seconds and that is reflect on web admin dashboard but I when I am trying to check on dashbard then sometime I am getting this error.
[response] => error
[exceptions] => Array
(
[0] => java.lang.RuntimeException: org.apache.phoenix.exception.PhoenixIOException
at org.apache.calcite.avatica.jdbc.JdbcResultSet.create(JdbcResultSet.java:98)
at org.apache.calcite.avatica.jdbc.JdbcMeta.execute(JdbcMeta.java:867)
at org.apache.calcite.avatica.remote.LocalService.apply(LocalService.java:268)
at org.apache.calcite.avatica.remote.Service$ExecuteRequest.accept(Service.java:1024)
at org.apache.calcite.avatica.remote.Service$ExecuteRequest.accept(Service.java:1000)
at org.apache.calcite.avatica.remote.AbstractHandler.apply(AbstractHandler.java:95)
at org.apache.calcite.avatica.remote.JsonHandler.apply(JsonHandler.java:52)
at org.apache.calcite.avatica.server.AvaticaJsonHandler.handle(AvaticaJsonHandler.java:129)
at org.apache.phoenix.shaded.org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52)
at org.apache.phoenix.shaded.org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
at org.apache.phoenix.shaded.org.eclipse.jetty.server.Server.handle(Server.java:499)
at org.apache.phoenix.shaded.org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:311)
at org.apache.phoenix.shaded.org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
at org.apache.phoenix.shaded.org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:544)
at org.apache.phoenix.shaded.org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635)
at org.apache.phoenix.shaded.org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.phoenix.exception.PhoenixIOException
at org.apache.phoenix.util.ServerUtil.parseServerException(ServerUtil.java:111)
at org.apache.phoenix.iterate.BaseResultIterators.getIterators(BaseResultIterators.java:808)
at org.apache.phoenix.iterate.BaseResultIterators.getIterators(BaseResultIterators.java:714)
at org.apache.phoenix.iterate.MergeSortResultIterator.getMinHeap(MergeSortResultIterator.java:72)
at org.apache.phoenix.iterate.MergeSortResultIterator.minIterator(MergeSortResultIterator.java:93)
at org.apache.phoenix.iterate.MergeSortResultIterator.next(MergeSortResultIterator.java:58)
at org.apache.phoenix.iterate.BaseGroupedAggregatingResultIterator.next(BaseGroupedAggregatingResultIterator.java:64)
at org.apache.phoenix.iterate.DelegateResultIterator.next(DelegateResultIterator.java:44)
at org.apache.phoenix.iterate.OffsetResultIterator.next(OffsetResultIterator.java:45)
at org.apache.phoenix.iterate.DelegateResultIterator.next(DelegateResultIterator.java:44)
at org.apache.phoenix.iterate.LimitingResultIterator.next(LimitingResultIterator.java:47)
at org.apache.phoenix.jdbc.PhoenixResultSet.next(PhoenixResultSet.java:778)
at org.apache.calcite.avatica.jdbc.JdbcResultSet.frame(JdbcResultSet.java:133)
at org.apache.calcite.avatica.jdbc.JdbcResultSet.create(JdbcResultSet.java:91)
... 16 more
Caused by: java.util.concurrent.CancellationException
at java.util.concurrent.FutureTask.report(FutureTask.java:121)
at java.util.concurrent.FutureTask.get(FutureTask.java:206)
at org.apache.phoenix.iterate.BaseResultIterators.getIterators(BaseResultIterators.java:766)
... 28 more
)
Each Batch Process it will take 30 records from table and update some information in table. I have used php json API to fetch records from HBase using phoenix. Please help me.
Thanks in advance.

BeanManager method getReference() is not available during application initialization

I am trying to deploy a war file into Wildfly 10.0.0.Final, the deployment fails with the following error :
"{\"WFLYCTL0080: Failed services\" => {\"jboss.deployment.unit.\\\"management-app.war\\\".WeldStartService\" => \"org.jboss.msc.service.StartException in service jboss.deployment.unit.\\\"management-app.war\\\".WeldStartService: Failed to start service
Caused by: org.jboss.weld.exceptions.DefinitionException: Exception List with 1 exceptions:
Exception 0 :
org.jboss.weld.exceptions.IllegalStateException: WELD-001332: BeanManager method getReference() is not available during application initialization
at org.jboss.weld.bean.builtin.BeanManagerProxy.checkContainerState(BeanManagerProxy.java:242)
at org.jboss.weld.bean.builtin.BeanManagerProxy.getReference(BeanManagerProxy.java:84)
at morpho.mcp.adapter.cdi.AdapterExtension.getAdapterDefinition(AdapterExtension.java:159)
at morpho.mcp.adapter.cdi.AdapterExtension.afterBeanDiscovery(AdapterExtension.java:109)
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.jboss.weld.injection.StaticMethodInjectionPoint.invoke(StaticMethodInjectionPoint.java:88)
at org.jboss.weld.injection.MethodInvocationStrategy$SpecialParamPlusBeanManagerStrategy.invoke(MethodInvocationStrategy.java:144)
at org.jboss.weld.event.ObserverMethodImpl.sendEvent(ObserverMethodImpl.java:309)
at org.jboss.weld.event.ExtensionObserverMethodImpl.sendEvent(ExtensionObserverMethodImpl.java:124)
at org.jboss.weld.event.ObserverMethodImpl.sendEvent(ObserverMethodImpl.java:287)
at org.jboss.weld.event.ObserverMethodImpl.notify(ObserverMethodImpl.java:265)
at org.jboss.weld.event.ObserverNotifier.notifySyncObservers(ObserverNotifier.java:271)
at org.jboss.weld.event.ObserverNotifier.notify(ObserverNotifier.java:260)
at org.jboss.weld.event.ObserverNotifier.fireEvent(ObserverNotifier.java:154)
at org.jboss.weld.event.ObserverNotifier.fireEvent(ObserverNotifier.java:148)
at org.jboss.weld.bootstrap.events.AbstractContainerEvent.fire(AbstractContainerEvent.java:53)
at org.jboss.weld.bootstrap.events.AbstractDefinitionContainerEvent.fire(AbstractDefinitionContainerEvent.java:42)
at org.jboss.weld.bootstrap.events.AfterBeanDiscoveryImpl.fire(AfterBeanDiscoveryImpl.java:61)
at org.jboss.weld.bootstrap.WeldStartup.deployBeans(WeldStartup.java:423)
at org.jboss.weld.bootstrap.WeldBootstrap.deployBeans(WeldBootstrap.java:83)
at org.jboss.as.weld.WeldStartService.start(WeldStartService.java:95)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1948)
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1881)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
\"}}"
Assuming that the war was working fine for JBoss AS7. What could be the possible root cause for such behavior ?
It seems that a WAR which is not a bean archive is missing the org.jboss.as.weld.WeldStartService dependency. But how can this issue be resolved ?

But how can this issue be resolved ?
Do not use BeanManager.getReference before AfterDeploymentValidation. Refactor your code accordingly. The reason is - getReference might give you incomplete results. At that point, the bootstrap is not yet done and getReference method might fail to retrieve a reference as there might not be one at a given time (although it would be there later on).
As for how to workaround this:
Use Weld non-portable mode although that might have more undesirable effects. You should firstly try to refactor the code before falling back to this configuration.

Apache Calcite is not working in Web Application

I'm using Apache Calcite in My Project to do CSV,Excel and Other Database management.
Its working when i execute through main method but its giving an error while executing through web service
Caused by: java.lang.RuntimeException: org.codehaus.commons.compiler.CompileException: Line 1, Column 0: package org.apache.calcite.rel.metadata does not exist (compiler.err.doesnt.exist)
at com.google.common.base.Throwables.propagate(Throwables.java:160)
at org.apache.calcite.rel.metadata.JaninoRelMetadataProvider.load3(JaninoRelMetadataProvider.java:361)
at org.apache.calcite.rel.metadata.JaninoRelMetadataProvider.access$000(JaninoRelMetadataProvider.java:94)
at org.apache.calcite.rel.metadata.JaninoRelMetadataProvider$1.load(JaninoRelMetadataProvider.java:113)
at org.apache.calcite.rel.metadata.JaninoRelMetadataProvider$1.load(JaninoRelMetadataProvider.java:110)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache.java:3937)
at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3941)
at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4824)
at org.apache.calcite.rel.metadata.JaninoRelMetadataProvider.create(JaninoRelMetadataProvider.java:448)
at org.apache.calcite.rel.metadata.JaninoRelMetadataProvider.revise(JaninoRelMetadataProvider.java:460)
at org.apache.calcite.rel.metadata.RelMetadataQuery.revise(RelMetadataQuery.java:186)
at org.apache.calcite.rel.metadata.RelMetadataQuery.collations(RelMetadataQuery.java:484)
at org.apache.calcite.rel.metadata.RelMdCollation.project(RelMdCollation.java:207)
at org.apache.calcite.rel.logical.LogicalProject$1.get(LogicalProject.java:117)
at org.apache.calcite.rel.logical.LogicalProject$1.get(LogicalProject.java:115)
at org.apache.calcite.plan.RelTraitSet.replaceIfs(RelTraitSet.java:238)
at org.apache.calcite.rel.logical.LogicalProject.create(LogicalProject.java:113)
at org.apache.calcite.rel.logical.LogicalProject.create(LogicalProject.java:103)
at org.apache.calcite.rel.core.RelFactories$ProjectFactoryImpl.createProject(RelFactories.java:120)
at org.apache.calcite.tools.RelBuilder.project(RelBuilder.java:853)
at org.apache.calcite.plan.RelOptUtil.createProject(RelOptUtil.java:2881)
at org.apache.calcite.plan.RelOptUtil.createProject(RelOptUtil.java:2839)
at org.apache.calcite.plan.RelOptUtil.createProject(RelOptUtil.java:2783)
at org.apache.calcite.sql2rel.SqlToRelConverter.convertSelectList(SqlToRelConverter.java:3495)
at org.apache.calcite.sql2rel.SqlToRelConverter.convertSelectImpl(SqlToRelConverter.java:665)
at org.apache.calcite.sql2rel.SqlToRelConverter.convertSelect(SqlToRelConverter.java:622)
at org.apache.calcite.sql2rel.SqlToRelConverter.convertQueryRecursive(SqlToRelConverter.java:2852)
at org.apache.calcite.sql2rel.SqlToRelConverter.convertQuery(SqlToRelConverter.java:556)
at org.apache.calcite.prepare.Prepare.prepareSql(Prepare.java:229)
at org.apache.calcite.prepare.Prepare.prepareSql(Prepare.java:193)
at org.apache.calcite.prepare.CalcitePrepareImpl.prepare2_(CalcitePrepareImpl.java:733)
at org.apache.calcite.prepare.CalcitePrepareImpl.prepare_(CalcitePrepareImpl.java:597)
at org.apache.calcite.prepare.CalcitePrepareImpl.prepareSql(CalcitePrepareImpl.java:567)
at org.apache.calcite.jdbc.CalciteConnectionImpl.parseQuery(CalciteConnectionImpl.java:215)
at org.apache.calcite.jdbc.CalciteMetaImpl.prepareAndExecute(CalciteMetaImpl.java:594)
at org.apache.calcite.avatica.AvaticaConnection.prepareAndExecuteInternal(AvaticaConnection.java:613)
at org.apache.calcite.avatica.AvaticaStatement.executeInternal(AvaticaStatement.java:139)
... 44 more

I think you're hitting CALCITE-1461, which will be fixed in Calcite 1.11. For now, disable shading.

Cassandra AssertionError

I received an OOM exception at one point in Cassandra. Mine is a single instance running on a modestly powered server, and i was doing some load testing, so no surprise there.
But, i have subsequently been unable to use the instance. When i list the keyspaces, only "system" is shown. But when i try to recreate the keyspace i was testing with, Hector responds with the dreaded "All host pools marked down. Retry burden pushed out to client." message, and the Cassandra log has the following stack trace:
ERROR [MigrationStage:1] 2012-04-27 20:47:00,863 AbstractCassandraDaemon.java (line 134) Exception in thread Thread[MigrationStage:1,5,main]
java.lang.AssertionError
at org.apache.cassandra.db.DefsTable.updateKeyspace(DefsTable.java:441)
at org.apache.cassandra.db.DefsTable.mergeKeyspaces(DefsTable.java:339)
at org.apache.cassandra.db.DefsTable.mergeSchema(DefsTable.java:269)
at org.apache.cassandra.service.MigrationManager$1.call(MigrationManager.java:214)
at java.util.concurrent.FutureTask$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)
ERROR [Thrift:9] 2012-04-27 20:47:00,864 CustomTThreadPoolServer.java (line 204) Error occurred during processing of message.
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.AssertionError
at org.apache.cassandra.utils.FBUtilities.waitOnFuture(FBUtilities.java:372)
at org.apache.cassandra.service.MigrationManager.announce(MigrationManager.java:191)
at org.apache.cassandra.service.MigrationManager.announceNewKeyspace(MigrationManager.java:129)
at org.apache.cassandra.thrift.CassandraServer.system_add_keyspace(CassandraServer.java:987)
at org.apache.cassandra.thrift.Cassandra$Processor$system_add_keyspace.getResult(Cassandra.java:3370)
at org.apache.cassandra.thrift.Cassandra$Processor$system_add_keyspace.getResult(Cassandra.java:3358)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:32)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:34)
at org.apache.cassandra.thrift.CustomTThreadPoolServer$WorkerProcess.run(CustomTThreadPoolServer.java:186)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.util.concurrent.ExecutionException: java.lang.AssertionError
at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at org.apache.cassandra.utils.FBUtilities.waitOnFuture(FBUtilities.java:368)
... 11 more
Caused by: java.lang.AssertionError
at org.apache.cassandra.db.DefsTable.updateKeyspace(DefsTable.java:441)
at org.apache.cassandra.db.DefsTable.mergeKeyspaces(DefsTable.java:339)
at org.apache.cassandra.db.DefsTable.mergeSchema(DefsTable.java:269)
at org.apache.cassandra.service.MigrationManager$1.call(MigrationManager.java:214)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
... 3 more
The old keyspace was still in the data dir, so i moved it, but that didn't help. It seems that the system data still has an invalid reference somewhere. Does anyone know how to fix this?
Edit: from the CLI, a "describe cluster;" only describes the "system" keyspace. But when i "use system;" and then "list schema_keyspaces;" the following is displayed:
Using default limit of 100
-------------------
RowKey: mango
=> (column=durable_writes, value=true, timestamp=29127788177516974)
=> (column=name, value=mango, timestamp=29127788177516974)
=> (column=strategy_class, value=org.apache.cassandra.locator.SimpleStrategy, timestamp=29127788177516974)
=> (column=strategy_options, value={"replication_factor":"1"}, timestamp=29127788177516974)
1 Row Returned.
Elapsed time: 1107 msec(s).
"mango" is the keyspace that i can no longer access, but it is still in there to some degree. Is there any way to fix it?

The problem almost certainly is that the recreated keyspace is inconsistent with the commit log or data stored with the original definition. Shut down the Cassandra server and clear out the commitlog, saved_caches, and data directory corresponding to the keyspace. The locations of these directories are in cassandra.yaml - look for data_file_directories, saved_caches_directory, and commitlog_directory.

This problem is due to inconsistency and you can go for following steps.
1) In your case this is OK to clear "data" , "saved_caches" and "commitlog" directories as you dont have any critical data and other Keyspaces.
2) In the scenarios where you have some critical data and you can not delete above mentioned directories do the following.
Use nodetool drain to Empty the commitlog on all the nodes of the cluster.
Then delete all the "LocationInfo*" files from "/data/system" directories and restart the cluster.