s.ar...@geophy.com
Feb 8, 2017, 5:57:19 AM2/8/17
to Stardog
Dear support, how do i recover stardog? I have 10 databases that are not display at the interface anymore. The files are in the filesystem.
I tried the command
$STARDOG/bin/stardog-admin db repair coredb
But I got the error:
Database 'coredb' does not exist.
Any command that can fix this?
s.ar...@geophy.com
Feb 8, 2017, 6:01:33 AM2/8/17
to Stardog, s.ar...@geophy.com
Here the log trace:
.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 65% complete in 00:00:31 (486.7K triples/sec)
INFO 2017-02-08 10:51:06,579 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 67% complete in 00:00:32 (483.9K triples/sec)
INFO 2017-02-08 10:51:07,648 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 68% complete in 00:00:33 (475.5K triples/sec)
INFO 2017-02-08 10:51:14,314 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 70% complete in 00:00:40 (408.4K triples/sec)
INFO 2017-02-08 10:51:22,240 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 71% complete in 00:00:48 (346.1K triples/sec)
INFO 2017-02-08 10:51:31,387 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 72% complete in 00:00:57 (295.0K triples/sec)
INFO 2017-02-08 10:51:41,158 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 73% complete in 00:01:07 (255.6K triples/sec)
INFO 2017-02-08 10:51:53,333 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 74% complete in 00:01:19 (219.3K triples/sec)
INFO 2017-02-08 10:52:01,618 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 75% complete in 00:01:27 (201.2K triples/sec)
INFO 2017-02-08 10:52:12,955 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 76% complete in 00:01:38 (180.5K triples/sec)
INFO 2017-02-08 10:52:14,001 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 77% complete in 00:01:39 (181.0K triples/sec)
INFO 2017-02-08 10:52:15,480 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 79% complete in 00:01:41 (183.0K triples/sec)
INFO 2017-02-08 10:52:16,900 [Stardog.Executor-266] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 81% complete in 00:01:42 (185.0K triples/sec)
INFO 2017-02-08 10:52:31,460 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 83% complete in 00:01:57 (166.1K triples/sec)
INFO 2017-02-08 10:52:32,862 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 84% complete in 00:01:58 (166.1K triples/sec)
INFO 2017-02-08 10:52:34,046 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 85% complete in 00:01:59 (166.4K triples/sec)
INFO 2017-02-08 10:52:35,652 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 87% complete in 00:02:01 (168.1K triples/sec)
INFO 2017-02-08 10:52:36,805 [Stardog.Executor-264] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 88% complete in 00:02:02 (168.4K triples/sec)
INFO 2017-02-08 10:52:41,434 [Stardog.Executor-236] com.complexible.stardog.StardogKernel:printInternal(314): Indexing triples: 100% complete in 00:02:07 (184.4K triples/sec)
INFO 2017-02-08 10:52:41,435 [Stardog.Executor-236] com.complexible.stardog.StardogKernel:stop(326):
INFO 2017-02-08 10:52:41,435 [Stardog.Executor-236] com.complexible.stardog.StardogKernel:stop(329): Indexing triples finished in 00:02:07.379
INFO 2017-02-08 10:53:06,830 [Stardog.Executor-271] com.complexible.stardog.StardogKernel:printInternal(314): Persisting dictionary: 100% complete in 00:00:25
INFO 2017-02-08 10:53:06,830 [Stardog.Executor-271] com.complexible.stardog.StardogKernel:stop(326):
INFO 2017-02-08 10:53:06,830 [Stardog.Executor-271] com.complexible.stardog.StardogKernel:stop(329): Persisting dictionary finished in 00:00:25.385
ERROR 2017-02-08 10:53:06,832 [Stardog.Executor-236] com.complexible.stardog.protocols.server.SPECServerFunction:query(536): There was an error executing query: prefix gn: <http://sws.geonames.org/>
prefix geo: <http://www.opengis.net/ont/geosparql#>
prefix sf: <http://www.opengis.net/def/sf/>
prefix g: <http://geophy.com/>
prefix ws: <http://www.w3.org/2003/01/geo/wgs84_pos#>
insert {
?s geo:hasGeometry ?geometry .
?geometry a sf:Point .
?geometry geo:asWKT ?point.
} where {
?s ws:lat ?lat .
?s ws:long ?lon .
bind(strdt(concat("Point(", str(?lon)," ", str(?lat),")"),geo:wktLiteral ) as ?point) .
bind(URI(concat("http://geophy.data/lon-lat/", str(?lon),"-", str(?lat) )) as ?geometry) .
}
com.complexible.stardog.plan.eval.operator.OperatorException: Query execution cancelled: Execution time exceeded query timeout 300000
at com.complexible.stardog.plan.eval.operator.impl.AbstractOperator.checkCanceled(AbstractOperator.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:129) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:25) ~[stardog-4.2.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.2.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.2.3.jar:?]
at com.google.common.collect.Iterators.size(Iterators.java:191) ~[guava-18.0.jar:?]
at com.complexible.stardog.plan.eval.QueryEngine.executeUpdate(QueryEngine.java:166) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DefaultQueryFactory$UpdateQueryImpl.execute(DefaultQueryFactory.java:263) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DefaultQueryFactory$UpdateQueryImpl.execute(DefaultQueryFactory.java:242) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DelegatingUpdateQuery.execute(DelegatingUpdateQuery.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$TimerPauseUpdate.execute(DatabaseImpl.java:1571) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$TimerPauseUpdate.execute(DatabaseImpl.java:1559) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DelegatingUpdateQuery.execute(DelegatingUpdateQuery.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.StardogKernel$SecuredUpdateQuery.execute(StardogKernel.java:3765) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.StardogKernel$SecuredUpdateQuery.execute(StardogKernel.java:3752) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.query(SPECServerFunction.java:526) ~[stardog-protocols-spec-server-4.2.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:152) ~[stardog-protocols-spec-server-4.2.3.jar:?]
at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:311) ~[stardog-protocols-api-server-4.2.3.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_121]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_121]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_121]
ERROR 2017-02-08 10:53:06,971 [Stardog.Executor-236] com.complexible.common.protocols.server.rpc.ServerHandler:exceptionCaught(401): exceptionCaughtServerHandler
com.complexible.stardog.plan.eval.operator.OperatorException: Query execution cancelled: Execution time exceeded query timeout 300000
at com.complexible.stardog.plan.eval.operator.impl.AbstractOperator.checkCanceled(AbstractOperator.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:129) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:25) ~[stardog-4.2.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.2.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.2.3.jar:?]
at com.google.common.collect.Iterators.size(Iterators.java:191) ~[guava-18.0.jar:?]
at com.complexible.stardog.plan.eval.QueryEngine.executeUpdate(QueryEngine.java:166) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DefaultQueryFactory$UpdateQueryImpl.execute(DefaultQueryFactory.java:263) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DefaultQueryFactory$UpdateQueryImpl.execute(DefaultQueryFactory.java:242) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DelegatingUpdateQuery.execute(DelegatingUpdateQuery.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$TimerPauseUpdate.execute(DatabaseImpl.java:1571) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$TimerPauseUpdate.execute(DatabaseImpl.java:1559) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DelegatingUpdateQuery.execute(DelegatingUpdateQuery.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.StardogKernel$SecuredUpdateQuery.execute(StardogKernel.java:3765) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.StardogKernel$SecuredUpdateQuery.execute(StardogKernel.java:3752) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.query(SPECServerFunction.java:526) ~[stardog-protocols-spec-server-4.2.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:152) ~[stardog-protocols-spec-server-4.2.3.jar:?]
at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:311) ~[stardog-protocols-api-server-4.2.3.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_121]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_121]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_121]
ERROR 2017-02-08 10:53:06,972 [StardogServer.WorkerGroup-1] com.complexible.stardog.protocols.http.server.HttpMessageEncoder:createErrorResponse(293): The result encoder received an error message it could not encode, error was:
com.complexible.stardog.plan.eval.operator.OperatorException: Query execution cancelled: Execution time exceeded query timeout 300000
at com.complexible.stardog.plan.eval.operator.impl.AbstractOperator.checkCanceled(AbstractOperator.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:129) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.plan.eval.operator.util.AutoCloseOperator.computeNext(AutoCloseOperator.java:25) ~[stardog-4.2.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.tryToComputeNext(AbstractSkippingIterator.java:143) ~[stardog-utils-common-4.2.3.jar:?]
at com.complexible.common.collect.AbstractSkippingIterator.hasNext(AbstractSkippingIterator.java:130) ~[stardog-utils-common-4.2.3.jar:?]
at com.google.common.collect.Iterators.size(Iterators.java:191) ~[guava-18.0.jar:?]
at com.complexible.stardog.plan.eval.QueryEngine.executeUpdate(QueryEngine.java:166) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DefaultQueryFactory$UpdateQueryImpl.execute(DefaultQueryFactory.java:263) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DefaultQueryFactory$UpdateQueryImpl.execute(DefaultQueryFactory.java:242) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DelegatingUpdateQuery.execute(DelegatingUpdateQuery.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$TimerPauseUpdate.execute(DatabaseImpl.java:1571) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.db.DatabaseImpl$TimerPauseUpdate.execute(DatabaseImpl.java:1559) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.query.DelegatingUpdateQuery.execute(DelegatingUpdateQuery.java:139) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.StardogKernel$SecuredUpdateQuery.execute(StardogKernel.java:3765) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.StardogKernel$SecuredUpdateQuery.execute(StardogKernel.java:3752) ~[stardog-4.2.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.query(SPECServerFunction.java:526) ~[stardog-protocols-spec-server-4.2.3.jar:?]
at com.complexible.stardog.protocols.server.SPECServerFunction.handleMessage(SPECServerFunction.java:152) ~[stardog-protocols-spec-server-4.2.3.jar:?]
at com.complexible.common.protocols.server.rpc.ServerHandler.lambda$handleMessage$1(ServerHandler.java:311) ~[stardog-protocols-api-server-4.2.3.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) ~[?:1.8.0_121]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[?:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[?:1.8.0_121]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[?:1.8.0_121]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_121]
INFO 2017-02-08 11:15:01,214 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(162): Initializing R2RML registry
INFO 2017-02-08 11:15:01,237 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(171): Loaded R2RML registry with 0 sources
Stardog home is currently locked, cannot start kernel. Multiple instances of Stardog cannot use the same home directory,
shutdown the current Stardog server before starting another. If no other server is running and the Stardog home directory
appears to be locked, you may remove the file '/data/stardog_data/system.lock' from your Stardog home directory to remove the lock.
INFO 2017-02-08 11:15:47,193 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(162): Initializing R2RML registry
INFO 2017-02-08 11:15:47,214 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(171): Loaded R2RML registry with 0 sources
Stardog home is currently locked, cannot start kernel. Multiple instances of Stardog cannot use the same home directory,
shutdown the current Stardog server before starting another. If no other server is running and the Stardog home directory
appears to be locked, you may remove the file '/data/stardog_data/system.lock' from your Stardog home directory to remove the lock.
INFO 2017-02-08 11:16:04,653 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(162): Initializing R2RML registry
INFO 2017-02-08 11:16:04,668 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(171): Loaded R2RML registry with 0 sources
INFO 2017-02-08 11:16:05,592 [main] com.complexible.stardog.StardogKernel:start(1871): Initializing Stardog
************************************************************
This copy of Stardog is licensed to Geophy Enterprise #1 (http://geophy.com), Geophy
This is a Enterprise license
This license will expire in 300 days on Tue Dec 05 13:38:59 CET 2017
************************************************************
:;
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************************************************************
Stardog server 4.2.3 started on Wed Feb 08 11:16:06 CET 2017.
Stardog server is listening on all network interfaces.
HTTP server available at http://localhost:5820.
STARDOG_HOME=/data/stardog_data
INFO 2017-02-08 11:16:06,008 [main] com.complexible.stardog.cli.impl.ServerStart:call(249): Memory options
INFO 2017-02-08 11:16:06,009 [main] com.complexible.stardog.cli.impl.ServerStart:call(250): Min Heap Size: 2.0G
INFO 2017-02-08 11:16:06,009 [main] com.complexible.stardog.cli.impl.ServerStart:call(251): Max Heap Size: 25G
INFO 2017-02-08 11:16:06,009 [main] com.complexible.stardog.cli.impl.ServerStart:call(252): Max Off-Heap : 12G
INFO 2017-02-08 11:16:06,009 [main] com.complexible.stardog.cli.impl.ServerStart:call(253): System Memory: 35G
INFO 2017-02-08 11:17:23,133 [Stardog.Executor-24] com.complexible.stardog.StardogKernel:shutdown(2119): Stardog server 4.2.3 shutdown on 2017-02-08T11:17:23.132+0100.
INFO 2017-02-08 11:17:56,219 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(162): Initializing R2RML registry
INFO 2017-02-08 11:17:56,237 [main] com.complexible.stardog.virtual.DefaultVirtualGraphRegistry:syncCache(171): Loaded R2RML registry with 0 sources
INFO 2017-02-08 11:17:56,857 [main] com.complexible.stardog.StardogKernel:start(1871): Initializing Stardog
Stephen Nowell
Feb 8, 2017, 9:10:33 AM2/8/17
to sta...@clarkparsia.com, s.ar...@geophy.com
Hi Samur,
We are currently transitioning our support over to Discourse. I have taken your report and created a topic over there in the Support section: https://community.stardog.com/t/stardog-recovery/75.
You'll find all future responses in that thread.
Cheers,
Stephen
We are currently transitioning our support over to Discourse. I have taken your report and created a topic over there in the Support section: https://community.stardog.com/t/stardog-recovery/75.
You'll find all future responses in that thread.
Cheers,
Stephen
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