Spatial index problem crashes server without recovery option

Support Bug
1

We have run into a issue where enabling a spatial index on a database causes the server to crash, restarting the server causes a immediate crash again.

ERROR 2017-07-26 11:24:37,547 [Stardog.Executor-0]  com.complexible.stardog.spatial.io.RDFGeospatialSource:lambda$parse$19(142): Failed to parse unknown/malformed shape: <http://www.opengis.net/def/crs/EPSG/0/28992> POINT(132569 517118)

I’ve tried moving the database directory outside the stardog data directory, the server complains about a missing database and stops as well.

WARN  2017-07-26 11:28:02,233 [main] com.complexible.stardog.db.DatabaseFactoryImpl:read(141): Database inspire is invalid and the repair failed: File (/home/stardog/data/inspire) is not a directory, could not find an index at this location
INFO  2017-07-26 11:28:02,234 [main] com.complexible.stardog.StardogKernel:initDatabases(2263): Database inspire will not be available because there was an error initializing the database: The index directory does not exist
ERROR 2017-07-26 11:28:02,986 [main] com.complexible.stardog.Stardog:initKernel(224): There was an error during kernel init
com.complexible.stardog.security.ResourceNotFoundException: Permission does not exist.
        at com.complexible.stardog.security.index.IndexAuthorizationManager.assertExists(IndexAuthorizationManager.java:203) ~[stardog-core-security-5.0.jar:?]
        at com.complexible.stardog.security.index.IndexAuthorizationManager.delete(IndexAuthorizationManager.java:312) ~[stardog-core-security-5.0.jar:?]
        at com.complexible.stardog.security.impl.SystemSecurityManagerImpl.delete(SystemSecurityManagerImpl.java:389) ~[stardog-core-security-5.0.jar:?]
        at com.complexible.stardog.security.index.IndexBackedSystemSecurityManager.delete(IndexBackedSystemSecurityManager.java:205) ~[stardog-core-security-5.0.jar:?]
        at com.complexible.stardog.security.StardogSecurityManagerImpl.delete(StardogSecurityManagerImpl.java:638) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.security.StardogSecurityManagerImpl.deleteUserPerm(StardogSecurityManagerImpl.java:123) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.StardogKernel.lambda$dbPermissions$20(StardogKernel.java:1992) ~[stardog-5.0.jar:?]
        at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) ~[shiro-core-1.2.3.jar:1.2.3]
        at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) ~[shiro-core-1.2.3.jar:1.2.3]
        at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) ~[shiro-core-1.2.3.jar:1.2.3]
        at com.complexible.stardog.StardogKernel.dbPermissions(StardogKernel.java:1987) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.StardogKernel.handleUnusableIndex(StardogKernel.java:2311) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.StardogKernel.initDatabases(StardogKernel.java:2272) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.StardogKernel.start(StardogKernel.java:2199) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.StardogKernel.initialize(StardogKernel.java:739) ~[stardog-5.0.jar:?]
        at com.complexible.stardog.Stardog.initKernel(Stardog.java:219) [stardog-5.0.jar:?]
        at com.complexible.stardog.Stardog.<init>(Stardog.java:211) [stardog-5.0.jar:?]
        at com.complexible.stardog.Stardog.<init>(Stardog.java:65) [stardog-5.0.jar:?]
        at com.complexible.stardog.Stardog$StardogBuilder.create(Stardog.java:560) [stardog-5.0.jar:?]
        at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:145) [stardog-cli-5.0.jar:?]
        at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:44) [stardog-cli-5.0.jar:?]
        at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55) [stardog-cli-5.0.jar:?]
        at com.complexible.stardog.cli.admin.CLI.main(CLI.java:182) [stardog-cli-5.0.jar:?]
Stardog could not be initialized: Permission does not exist.
Permission does not exist.
Waiting for running tasks to complete....done. Executor service has been shut down.

Can I disable the spatial index from command line ?

Any help greatly appreciated!

Bart

2

You should be able to disable the spatial index from the command line but it requires that Stardog to be running so that you can take the database offline. I don’t know when it’s crashing during startup but you might be able to Start Stardog and take the db offline in a single command so hopeefully it gets taken offline before it reaches the point where it crashes.

stardog-admin server start && stardog-admin db offline --timeout 0 myDb

then disable the index

stardog-admin metadata set -o spatial.enabled=false -- myDb

I’m sure the Stardog folks would be very interested to see what’s in the logs during the parse error.

3

You are very correct about that!

@semanticfire You can move the database directory outside of your STARDOG_HOME, just create an empty directory to replace it and you can avoid the server complaints.

4

Hi Bart,

Can you share with us the stack trace of how Stardog is crashing and unable to restart?
Is it related to that Failed to parse unknown/malformed shape error log?

5

where can I send you the logfile ?

6

Send it to my email: pedro@stardog.com
Thanks!

7

done

BTW, it is still 5.0 I haven’t had the time to test 5.0.1 due to travel and holidays