Sorry for the vague title. I'm not quite sure how to describe exactly what's wrong here other than something seems to have gone terribly wrong. I was loading the thompson/reuters (now Rveteve or some crazy new name) permid data and during loading I got the following error.
WARN 2019-11-07 20:17:16,994 [Stardog.Executor-0] com.complexible.common.rdf.rio.RDFStreamProcessor:setException(599): Error during loading /home/centos/Downloads/OpenPermID-bulk-person-20191103_092405.ttl.gz: Namespace prefix 'skos' used but not defined [L9]
WARN 2019-11-07 20:17:16,994 [Stardog.Executor-0] com.complexible.common.rdf.rio.RDFStreamProcessor:setException(606): Parse process creator:
java.lang.Exception: null
at com.complexible.common.rdf.rio.RDFStreamProcessor.<init>(RDFStreamProcessor.java:137) ~[stardog-utils-rdf-7.0.2.jar:?]
at com.complexible.common.rdf.rio.RDFStreamProcessor.create(RDFStreamProcessor.java:113) ~[stardog-utils-rdf-7.0.2.jar:?]
at com.complexible.stardog.index.StardogIndexLoader.loader(StardogIndexLoader.java:76) ~[stardog-7.0.2.jar:?]
at com.complexible.stardog.StardogKernel.bulkLoad(StardogKernel.java:1211) ~[stardog-7.0.2.jar:?]
at com.complexible.stardog.StardogKernel.createDatabase(StardogKernel.java:1381) ~[stardog-7.0.2.jar:?]
at com.complexible.stardog.protocols.http.server.AdminDatabaseService.createNewDatabase(AdminDatabaseService.java:539) ~[stardog-protocols-http-server-7.0.2.jar:?]
at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-7.0.2.jar:?]
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) ~[shiro-core-1.3.0.jar:1.3.0]
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) ~[shiro-core-1.3.0.jar:1.3.0]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_222]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_222]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_222]
No biggie. So there's an undefined prefix in there. It powered on....
INFO 2019-11-07 20:17:28,043 [Stardog.Executor-0] com.complexible.stardog.index.Index:printInternal(314): Parsing triples: 0% complete in 00:00:11 (2.0M triples - 178.7K triples/sec)
INFO 2019-11-07 20:17:32,406 [Stardog.Executor-0] com.complexible.stardog.index.Index:printInternal(314): Parsing triples: 1% complete in 00:00:15 (2.5M triples - 163.3K triples/sec)
Then Stardog just crashed with nothing in the logs but when I went to start it up again and try loading the data again I get the following errors in the logs
ERROR 2019-11-07 20:23:27,482 [stardog-user-1] com.complexible.stardog.StardogKernel:bulkLoad(1197): Unable to create loader for database.
com.complexible.mvcc.api.WriteConflictException: Drop conflicts with other create operation
at com.stardog.starrocks.index.VersionedDatabaseManager.drop(VersionedDatabaseManager.java:199) ~[stardog-7.0.2.jar:?]
at com.stardog.starrocks.NativeStorageKernel.drop(NativeStorageKernel.java:200) ~[stardog-7.0.2.jar:?]
at com.complexible.stardog.index.disk.rocks.RocksConcurrentIndexLoader.<init>(RocksConcurrentIndexLoader.java:156) ~[stardog-7.0.2.jar:?]
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_222]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[?:1.8.0_222]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:1.8.0_222]
at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[?:1.8.0_222]
at com.google.inject.internal.DefaultConstructionProxyFactory$2.newInstance(DefaultConstructionProxyFactory.java:86) ~[guice-4.0.jar:?]
at com.google.inject.internal.ConstructorInjector.provision(ConstructorInjector.java:105) ~[guice-4.0.jar:?]
at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85) ~[guice-4.0.jar:?]
at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:267) ~[guice-4.0.jar:?]
at com.google.inject.internal.InjectorImpl$2$1.call(InjectorImpl.java:1016) ~[guice-4.0.jar:?]
at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1092) ~[guice-4.0.jar:?]
at com.google.inject.internal.InjectorImpl$2.get(InjectorImpl.java:1012) ~[guice-4.0.jar:?]
at com.google.inject.assistedinject.FactoryProvider2.invoke(FactoryProvider2.java:770) ~[guice-assistedinject-4.0.jar:?]
at com.sun.proxy.$Proxy38.createDiskIndexBulkLoader(Unknown Source) ~[?:?]
at com.complexible.stardog.StardogKernel.bulkLoad(StardogKernel.java:1194) ~[stardog-7.0.2.jar:?]
at com.complexible.stardog.StardogKernel.createDatabase(StardogKernel.java:1381) ~[stardog-7.0.2.jar:?]
at com.complexible.stardog.protocols.http.server.AdminDatabaseService.createNewDatabase(AdminDatabaseService.java:539) ~[stardog-protocols-http-server-7.0.2.jar:?]
at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-7.0.2.jar:?]
at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.3.0.jar:1.3.0]
at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.3.0.jar:1.3.0]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_222]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_222]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_222]
ERROR 2019-11-07 20:23:27,505 [stardog-user-1] com.stardog.http.server.undertow.ErrorHandling:writeError(138): Unexpected error on the server
com.complexible.stardog.StardogException: Unable to create loader for database.
It seems like something is in a bad state. I couldn't quite follow the logs but I what I think was happening was I was loading from multiple *.gz files and they were loading in parallel so I'm not quite sure when exactly it failed.