Exception in thread "main" java.lang.Error message

[olivia solis]

Hello all,

I use OpenRefine a lot for my job. Specifically, LODRefine. I've installed a few plugins in the extension folder... VIB Bits. A few others. We have set up a Linux VM that is hosted remotely with the program, which is running in on a computer in a background state. Tonight while dealing with particularly large datasets that kept freezing the program, LODRefine, running remotely, shut down on me. I tried to reboot it from my Terminal window using ./refine which has worked for me consistently in the past.

However, I get the following error now:

Starting LODRefine at 'http://127.0.0.1:3333/'

20:39:38.014 [            refine_server] Starting Server bound to '127.0.0.1:3333' (0ms)

20:39:38.016 [            refine_server] refine.memory size: 4000m JVM Max heap: 3728736256 (2ms)

20:39:38.026 [            refine_server] Initializing context: '/' from '/usr/local/LOD_refine/LODRefine-master/main/webapp' (10ms)

20:39:38.070 [            refine_server] Starting autoreloading scanner...  (44ms)

20:39:45.552 [                   refine] Starting LODRefine 2.6 [TRUNK]... (7482ms)

20:39:47.210 [            crowdsourcing] Initializing crowdsourcing extension... (1658ms)

20:39:47.879 [            rdf-extension] Initializing rdf extension (669ms)

20:39:47.880 [            rdf-extension] Initializing endpoint manager (1ms)

Exception in thread "main" java.lang.Error: class org.apache.lucene.store.LockObtainFailedException: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/root/.local/share/openrefine/cache/rdfExtension/export/luceneIndex/write.lock

at org.mozilla.javascript.Context.throwAsScriptRuntimeEx(Context.java:1777)

at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:183)

at org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:247)

at org.mozilla.javascript.optimizer.OptRuntime.call1(OptRuntime.java:66)

at org.mozilla.javascript.gen.c6._c4(file:/usr/local/LOD_refine/LODRefine-master/main/webapp/../../extensions/rdf-extension/module/MOD-INF/controller.js:103)

at org.mozilla.javascript.gen.c6.call(file:/usr/local/LOD_refine/LODRefine-master/main/webapp/../../extensions/rdf-extension/module/MOD-INF/controller.js)

at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:398)

at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3065)

at org.mozilla.javascript.gen.c6.call(file:/usr/local/LOD_refine/LODRefine-master/main/webapp/../../extensions/rdf-extension/module/MOD-INF/controller.js)

at edu.mit.simile.butterfly.ButterflyModuleImpl.scriptInit(ButterflyModuleImpl.java:636)

at edu.mit.simile.butterfly.ButterflyModuleImpl.init(ButterflyModuleImpl.java:94)

at edu.mit.simile.butterfly.Butterfly.initializeModule(Butterfly.java:476)

at edu.mit.simile.butterfly.Butterfly.configure(Butterfly.java:451)

at edu.mit.simile.butterfly.Butterfly.init(Butterfly.java:308)

at org.mortbay.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:440)

at org.mortbay.jetty.servlet.ServletHolder.doStart(ServletHolder.java:263)

at com.google.refine.RefineServer.configure(Refine.java:296)

at com.google.refine.RefineServer.init(Refine.java:210)

at com.google.refine.Refine.init(Refine.java:117)

at com.google.refine.Refine.main(Refine.java:111)

I had a lot of problems finding the right combination of plugins/OpenRefine versions that led to the application performing as I needed it to perform. The RDF extension (and its autocomplete/Search for match feature) is somewhat critical to my job, though I know that the plugin is unfortunately not supported anymore. LODRefine seemed to be the answer to all my problems, until this. I have about 6 months of work saved in the program that I can't afford to lose. Any suggestions for troubleshooting would be very welcome!

Thank you,

Olivia 

[Ettore Rizza]

Hi Olivia,

I'm not a computer scientist, but I understand that the problem is with the write.lock file (root/.local/share/openrefine/cache/rdfExtension/export/luceneIndex/write.lock). It seems that this file was created because of the crash and that it should be deleted. 

But I would prefer to wait for another opinion before advising you to delete anything...

[Antonin Delpeuch (lists)]

Hi Olivia,

I agree with Ettore - you can try deleting the lock file, but I would
first back up the whole workspace to another directory first.

If this fails, you should still be able to create a fresh workspace and
reimport projects from your previous workspace - so I do not think your
data is at risk.

Cheers,
Antonin

On 02/08/2017 08:51, Ettore Rizza wrote:
> Hi Olivia,
>
> I'm not a computer scientist, but I understand that the problem is with
> the write.lock file
> (root/.local/share/openrefine/cache/rdfExtension/export/luceneIndex/write.lock).
> It seems that this file was created because of the crash and that it
> should be deleted

> <https://stackoverflow.com/questions/2341163/why-is-my-lucene-index-getting-locked>.

>
> But I would prefer to wait for another opinion before advising you to
> delete anything...
>
> Le mercredi 2 août 2017 04:25:58 UTC+2, olivia solis a écrit :
>
> Hello all,
> I use OpenRefine a lot for my job. Specifically, LODRefine. I've
> installed a few plugins in the extension folder... VIB Bits. A few
> others. We have set up a Linux VM that is hosted remotely with the
> program, which is running in on a computer in a background state.
> Tonight while dealing with particularly large datasets that kept
> freezing the program, LODRefine, running remotely, shut down on me.
> I tried to reboot it from my Terminal window using ./refine which
> has worked for me consistently in the past.
>
> However, I get the following error now:
>
> Starting LODRefine at 'http://127.0.0.1:3333/'
>
>
> 20:39:38.014 [ refine_server] Starting Server

> bound to '127.0.0.1:3333 <http://127.0.0.1:3333>' (0ms)

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