materialising a virtual graph

[PaulZH]

stardog 4.1.1

talking to a ms sql server

I'm trying to materialise a virtual graph.

I did 8 attempts and all failed, but not always due to the same reasons.

The same materialisation run from -ontop- to the file system worked at first attempt (more than 7 million triples in 1,5 hour).

Command used.

./stardog-admin virtual import --format r2rml -v CRAB /Users/Paul/Desktop/crab/CRAB.properties /Users/Paul/Desktop/crab/crab.r2rml.ttl 

Three types of errors encountered:

- error during indexing

- connection reset

- query timeout (timeout: 1h)

- error during indexing

There was a fatal failure during preparation of c8b9f0ef-314c-44b6-a3f9-9e089410e68b There was an error while indexing the new data
The detailed stack trace for the error is:
com.complexible.stardog.cli.CliException: There was a fatal failure during preparation of c8b9f0ef-314c-44b6-a3f9-9e089410e68b There was an error while indexing the new data
at com.complexible.stardog.cli.impl.ConnectionCommand.call(ConnectionCommand.java:76)
at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55)
at com.complexible.stardog.cli.admin.CLI.main(CLI.java:171)
Caused by: com.complexible.stardog.StardogException: There was a fatal failure during preparation of c8b9f0ef-314c-44b6-a3f9-9e089410e68b There was an error while indexing the new data
at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:86)
at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:34)
at com.complexible.stardog.api.impl.SPECUpdateQuery.execute(SPECUpdateQuery.java:43)
at com.complexible.stardog.api.impl.SPECUpdateQuery.execute(SPECUpdateQuery.java:26)
at com.complexible.stardog.virtual.cli.VirtualGraphImport.execute(VirtualGraphImport.java:138)
at com.complexible.stardog.cli.impl.ConnectionCommand.call(ConnectionCommand.java:61)
... 2 more
 
Caused by: com.complexible.common.protocols.client.ClientException: There was a fatal failure during preparation of c8b9f0ef-314c-44b6-a3f9-9e089410e68b There was an error while indexing the new data
at com.complexible.common.protocols.client.rpc.DefaultRPCClient.get(DefaultRPCClient.java:278)
at com.complexible.common.protocols.client.rpc.DefaultRPCClient.execute(DefaultRPCClient.java:254)
at com.complexible.stardog.protocols.snarl.client.AbstractSNARLClient.update(AbstractSNARLClient.java:168)
at com.complexible.stardog.protocols.snarl.client.AbstractSNARLClient.update(AbstractSNARLClient.java:60)
at com.complexible.stardog.api.impl.SPECUpdateQuery.execute(SPECUpdateQuery.java:40)
... 5 more
 
Caused by: java.lang.Exception: There was a fatal failure during preparation of c8b9f0ef-314c-44b6-a3f9-9e089410e68b There was an error while indexing the new data
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
at com.complexible.barc.DefaultThrowableCodec.decode(DefaultThrowableCodec.java:90)
at com.complexible.barc.BigPacketCodec.toException(BigPacketCodec.java:393)
at com.complexible.barc.BigPacketCodec.decode(BigPacketCodec.java:364)
at com.complexible.barc.BigPacketDecoder.channelRead(BigPacketDecoder.java:90)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)
at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:265)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:846)
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:112)
at java.lang.Thread.run(Thread.java:745)

- connection reset

The detailed stack trace for the error is:
com.complexible.stardog.cli.CliException: com.microsoft.sqlserver.jdbc.SQLServerException: Connection reset
at com.complexible.stardog.cli.impl.ConnectionCommand.call(ConnectionCommand.java:76)
at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55)
at com.complexible.stardog.cli.admin.CLI.main(CLI.java:171)
 
Caused by: com.complexible.stardog.StardogException: com.microsoft.sqlserver.jdbc.SQLServerException: Connection reset
at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:86)
at com.complexible.stardog.protocols.client.SPECClientUtil.toStardogException(SPECClientUtil.java:34)
at com.complexible.stardog.api.impl.SPECUpdateQuery.execute(SPECUpdateQuery.java:43)
at com.complexible.stardog.api.impl.SPECUpdateQuery.execute(SPECUpdateQuery.java:26)
at com.complexible.stardog.virtual.cli.VirtualGraphImport.execute(VirtualGraphImport.java:138)
at com.complexible.stardog.cli.impl.ConnectionCommand.call(ConnectionCommand.java:61)
 
... 2 more
 
Caused by: com.complexible.common.protocols.client.ClientException: com.microsoft.sqlserver.jdbc.SQLServerException: Connection reset
at com.complexible.common.protocols.client.rpc.DefaultRPCClient.get(DefaultRPCClient.java:278)
at com.complexible.common.protocols.client.rpc.DefaultRPCClient.execute(DefaultRPCClient.java:254)
at com.complexible.stardog.protocols.snarl.client.AbstractSNARLClient.update(AbstractSNARLClient.java:168)
at com.complexible.stardog.protocols.snarl.client.AbstractSNARLClient.update(AbstractSNARLClient.java:60)
at com.complexible.stardog.api.impl.SPECUpdateQuery.execute(SPECUpdateQuery.java:40)
 
... 5 more
 
Caused by: java.lang.Exception: com.microsoft.sqlserver.jdbc.SQLServerException: Connection reset
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
at com.complexible.barc.DefaultThrowableCodec.decode(DefaultThrowableCodec.java:90)
at com.complexible.barc.BigPacketCodec.toException(BigPacketCodec.java:393)
at com.complexible.barc.BigPacketCodec.decode(BigPacketCodec.java:364)
at com.complexible.barc.BigPacketDecoder.channelRead(BigPacketDecoder.java:90)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)
at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:265)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294)
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:846)
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:112)
at java.lang.Thread.run(Thread.java:745)

[Zachary Whitley]

I think I can help with two. There are database options for query.timeout and it isn't in the docs but the javadocs list an option for CONNECTION_TIMEOUT so you might want to see if you can set a connection.timeout option. The default for query.timeout is 5 minutes. It's set with a number followed by a letter s/m/h for seconds, minutes, or hours. 

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[PaulZH]

Thanks. I will check the connection timeout.

The query timeout was already set to 1h.

Paul