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From Danilo Tomasoni <tomas...@cosbi.eu>
Subject Re: misteriuos nullpointerexception while adding documents
Date Wed, 13 Feb 2019 10:51:05 GMT
I changed the schema, but I deleted all the documents and tried a reindex.

I also tried deleting the core and re-adding it.

The autocommit is disabled because hard commits are controlled in the 
client-side.

I also tried with a plain solr installation (just unpack solr and copy 
the index folder), and in this way it works.

In my production environment, If I create a new core with exactly the 
same configuration it doesn't ( I mean, after a couple of POST the error 
I sent you appears in the logs and the core is stopped and reloaded).

Any clue?

Thank you for your suggestions

Danilo

On 12/02/19 18:09, Erick Erickson wrote:
> bq. I disabled autocommit (both soft and hard), but used to work with a
> previous version of the schema.
>
>
> First, did you _change_ the schema without
> 1> deleting all the docs in the index
> 2> reindexing everything
>
> or better, indexing to a new collection and aliasing to it?
>
> If you changed the schema and continued indexing to the
> collection _at any time in the past_ you may have
> inconsistent merged segments. The only way to fix this
> is to re-index, and I strongly recommend to a new
> collection.
>
> Second:
> do _not_ disable, commits and index for a long time.
> 1> your tlog will grow forever until you do a hard commit
> 2> certain internal Solr structures grow until a new searcher
>      is opened, either soft commit or hard-commit-with-opensearcher-true
>
> https://lucidworks.com/2013/08/23/understanding-transaction-logs-softcommit-and-commit-in-sorlcloud/
>
> Best,
> Erick
>
> On Tue, Feb 12, 2019 at 1:03 AM MUNENDRA S.N <sn.munendra52@gmail.com> wrote:
>> Are you trying to set some field to null in the request?? Also, is that
>> particular field numeric, doc valued enabled and stored set to false??
>> Sharing more details would help here, specifically update request and
>> schema for those fields.
>>
>> Regards,
>> Munendra S N
>>
>>
>> On Tue, Feb 12, 2019 at 2:24 PM Danilo Tomasoni <tomasoni@cosbi.eu> wrote:
>>
>>> Hello all,
>>>
>>> I get this error while uploading my documents with 'set' modifier in
>>> json format.
>>>
>>> My solr version is 7.3.1.
>>>
>>> I disabled autocommit (both soft and hard), but used to work with a
>>> previous version of the schema.
>>>
>>> Someone have any clue on what's going on here?
>>>
>>> I can't reproduce the issue indexing locally on another solr 7.3.1
>>> instance, I get this error only in the production instance.
>>>
>>> Thank you
>>>
>>> Danilo
>>>
>>>
>>> ======== This is the error I get from client ========
>>>
>>>
>>> {
>>>     "responseHeader":{
>>>       "status":500,
>>>       "QTime":33},
>>>     "error":{
>>>       "trace":"
>>>
>>> java.lang.NullPointerException
>>>       at org.apache.solr.update.UpdateLog.lookup(UpdateLog.java:971)
>>>       at
>>>
>>> org.apache.solr.handler.component.RealTimeGetComponent.getInputDocumentFromTlog(RealTimeGetComponent.java:537)
>>>       at
>>>
>>> org.apache.solr.handler.component.RealTimeGetComponent.getInputDocument(RealTimeGetComponent.java:617)
>>>       at
>>>
>>> org.apache.solr.handler.component.RealTimeGetComponent.getInputDocument(RealTimeGetComponent.java:594)
>>>       at
>>>
>>> org.apache.solr.update.processor.DistributedUpdateProcessor.getUpdatedDocument(DistributedUpdateProcessor.java:1330)
>>>       at
>>>
>>> org.apache.solr.update.processor.DistributedUpdateProcessor.versionAdd(DistributedUpdateProcessor.java:1049)
>>>       at
>>>
>>> org.apache.solr.update.processor.DistributedUpdateProcessor.processAdd(DistributedUpdateProcessor.java:633)
>>>       at
>>>
>>> org.apache.solr.update.processor.LogUpdateProcessorFactory$LogUpdateProcessor.processAdd(LogUpdateProcessorFactory.java:103)
>>>       at
>>>
>>> org.apache.solr.update.processor.UpdateRequestProcessor.processAdd(UpdateRequestProcessor.java:55)
>>>       at
>>>
>>> org.apache.solr.update.processor.FieldMutatingUpdateProcessor.processAdd(FieldMutatingUpdateProcessor.java:118)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.handleAdds(JsonLoader.java:501)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.processUpdate(JsonLoader.java:145)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.load(JsonLoader.java:121)
>>>       at org.apache.solr.handler.loader.JsonLoader.load(JsonLoader.java:84)
>>>       at
>>>
>>> org.apache.solr.handler.UpdateRequestHandler$1.load(UpdateRequestHandler.java:97)
>>>       at
>>>
>>> org.apache.solr.handler.ContentStreamHandlerBase.handleRequestBody(ContentStreamHandlerBase.java:68)
>>>       at
>>>
>>> org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:195)
>>>       at org.apache.solr.core.SolrCore.execute(SolrCore.java:2503)
>>>       at org.apache.solr.servlet.HttpSolrCall.execute(HttpSolrCall.java:711)
>>>       at org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:517)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:384)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:330)
>>>       at
>>>
>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
>>>       at
>>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:219)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:126)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at org.eclipse.jetty.server.Server.handle(Server.java:530)
>>>       at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347)
>>>       at
>>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256)
>>>       at
>>> org.eclipse.jetty.io
>>> .AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
>>>       at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102)
>>>       at
>>> org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626)
>>>       at java.lang.Thread.run(Thread.java:748)
>>> "
>>>
>>> }
>>>
>>>
>>>    ======= this is the error I see in solr.log ===============
>>>
>>>
>>> 2019-02-12 08:43:01.592 INFO  (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.u.p.LogUpdateProcessorFactory [COSBIBioIndex]  webapp=/solr
>>> path=/update/json params={}{add=[PUBMEDPMID24951927
>>> (1625251880396390400), PUBMEDPMID19328818 (1625251880437284864),
>>> PUBMEDPMID24304416 (1625251880442527744), PUBMEDPMID24398789
>>> (1625251880446722048), PUBMEDPMID23111281 (1625251880455110656),
>>> PUBMEDPMID26933085 (1625251880464547840), PUBMEDPMID18635358
>>> (1625251880471887872), PUBMEDPMID26856594 (1625251880472936448),
>>> PUBMEDPMID21803289 (1625251880479227904), PUBMEDPMID25722448
>>> (1625251880487616512), ... (194 adds)]} 0 5567
>>> 2019-02-12 08:43:01.594 ERROR (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.h.RequestHandlerBase org.eclipse.jetty.io.EofException: Early EOF
>>>       at org.eclipse.jetty.server.HttpInput$3.getError(HttpInput.java:1126)
>>>       at org.eclipse.jetty.server.HttpInput$3.noContent(HttpInput.java:1115)
>>>       at org.eclipse.jetty.server.HttpInput.read(HttpInput.java:309)
>>>       at
>>>
>>> org.apache.commons.io.input.ProxyInputStream.read(ProxyInputStream.java:100)
>>>       at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
>>>       at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
>>>       at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
>>>       at java.io.InputStreamReader.read(InputStreamReader.java:184)
>>>       at org.noggit.JSONParser.fill(JSONParser.java:208)
>>>       at org.noggit.JSONParser.getMore(JSONParser.java:215)
>>>       at org.noggit.JSONParser.readStringChars2(JSONParser.java:709)
>>>       at org.noggit.JSONParser.readStringChars(JSONParser.java:689)
>>>       at org.noggit.JSONParser.getStringChars(JSONParser.java:1154)
>>>       at org.noggit.JSONParser.getString(JSONParser.java:1142)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseSingleFieldValue(JsonLoader.java:637)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseArrayFieldValue(JsonLoader.java:667)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseNormalFieldValue(JsonLoader.java:625)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseExtendedFieldValue(JsonLoader.java:599)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseFieldValue(JsonLoader.java:557)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseDoc(JsonLoader.java:543)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.handleAdds(JsonLoader.java:500)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.processUpdate(JsonLoader.java:145)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.load(JsonLoader.java:121)
>>>       at org.apache.solr.handler.loader.JsonLoader.load(JsonLoader.java:84)
>>>       at
>>>
>>> org.apache.solr.handler.UpdateRequestHandler$1.load(UpdateRequestHandler.java:97)
>>>       at
>>>
>>> org.apache.solr.handler.ContentStreamHandlerBase.handleRequestBody(ContentStreamHandlerBase.java:68)
>>>       at
>>>
>>> org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:195)
>>>       at org.apache.solr.core.SolrCore.execute(SolrCore.java:2503)
>>>       at org.apache.solr.servlet.HttpSolrCall.execute(HttpSolrCall.java:711)
>>>       at org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:517)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:384)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:330)
>>>       at
>>>
>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
>>>       at
>>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:219)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:126)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at org.eclipse.jetty.server.Server.handle(Server.java:530)
>>>       at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347)
>>>       at
>>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256)
>>>       at
>>> org.eclipse.jetty.io
>>> .AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
>>>       at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102)
>>>       at org.eclipse.jetty.io
>>> .ChannelEndPoint$2.run(ChannelEndPoint.java:124)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:382)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626)
>>>       at java.lang.Thread.run(Thread.java:748)
>>>
>>> 2019-02-12 08:43:01.599 ERROR (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.s.HttpSolrCall null:org.eclipse.jetty.io.EofException: Early EOF
>>>       at org.eclipse.jetty.server.HttpInput$3.getError(HttpInput.java:1126)
>>>       at org.eclipse.jetty.server.HttpInput$3.noContent(HttpInput.java:1115)
>>>       at org.eclipse.jetty.server.HttpInput.read(HttpInput.java:309)
>>>       at
>>>
>>> org.apache.commons.io.input.ProxyInputStream.read(ProxyInputStream.java:100)
>>>       at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
>>>       at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
>>>       at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
>>>       at java.io.InputStreamReader.read(InputStreamReader.java:184)
>>>       at org.noggit.JSONParser.fill(JSONParser.java:208)
>>>       at org.noggit.JSONParser.getMore(JSONParser.java:215)
>>>       at org.noggit.JSONParser.readStringChars2(JSONParser.java:709)
>>>       at org.noggit.JSONParser.readStringChars(JSONParser.java:689)
>>>       at org.noggit.JSONParser.getStringChars(JSONParser.java:1154)
>>>       at org.noggit.JSONParser.getString(JSONParser.java:1142)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseSingleFieldValue(JsonLoader.java:637)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseArrayFieldValue(JsonLoader.java:667)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseNormalFieldValue(JsonLoader.java:625)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseExtendedFieldValue(JsonLoader.java:599)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseFieldValue(JsonLoader.java:557)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.parseDoc(JsonLoader.java:543)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.handleAdds(JsonLoader.java:500)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.processUpdate(JsonLoader.java:145)
>>>       at
>>>
>>> org.apache.solr.handler.loader.JsonLoader$SingleThreadedJsonLoader.load(JsonLoader.java:121)
>>>       at org.apache.solr.handler.loader.JsonLoader.load(JsonLoader.java:84)
>>>       at
>>>
>>> org.apache.solr.handler.UpdateRequestHandler$1.load(UpdateRequestHandler.java:97)
>>>       at
>>>
>>> org.apache.solr.handler.ContentStreamHandlerBase.handleRequestBody(ContentStreamHandlerBase.java:68)
>>>       at
>>>
>>> org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:195)
>>>       at org.apache.solr.core.SolrCore.execute(SolrCore.java:2503)
>>>       at org.apache.solr.servlet.HttpSolrCall.execute(HttpSolrCall.java:711)
>>>       at org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:517)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:384)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:330)
>>>       at
>>>
>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
>>>       at
>>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:219)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:126)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at org.eclipse.jetty.server.Server.handle(Server.java:530)
>>>       at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347)
>>>       at
>>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256)
>>>       at
>>> org.eclipse.jetty.io
>>> .AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
>>>       at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102)
>>>       at org.eclipse.jetty.io
>>> .ChannelEndPoint$2.run(ChannelEndPoint.java:124)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:382)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626)
>>>       at java.lang.Thread.run(Thread.java:748)
>>>
>>> 2019-02-12 08:43:01.599 INFO  (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.c.SolrCore [COSBIBioIndex]  CLOSING SolrCore
>>> org.apache.solr.core.SolrCore@44e058fb
>>> 2019-02-12 08:43:01.600 INFO  (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.m.SolrMetricManager Closing metric reporters for
>>> registry=solr.core.COSBIBioIndex, tag=1155553531
>>> 2019-02-12 08:43:01.600 INFO  (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.u.DirectUpdateHandler2 Committing on IndexWriter close.
>>> 2019-02-12 08:43:01.600 INFO  (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.u.SolrIndexWriter Calling setCommitData with
>>> IW:org.apache.solr.update.SolrIndexWriter@13750f6d commitCommandVersion:0
>>> 2019-02-12 08:43:02.915 ERROR (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.u.DirectUpdateHandler2 Error in final commit
>>> java.lang.NoClassDefFoundError:
>>> org/apache/lucene/index/BufferedUpdatesStream$ApplyDeletesResult
>>>       at
>>>
>>> org.apache.lucene.index.BufferedUpdatesStream.closeSegmentStates(BufferedUpdatesStream.java:368)
>>>       at
>>>
>>> org.apache.lucene.index.FrozenBufferedUpdates.finishApply(FrozenBufferedUpdates.java:402)
>>>       at
>>>
>>> org.apache.lucene.index.FrozenBufferedUpdates.apply(FrozenBufferedUpdates.java:327)
>>>       at
>>>
>>> org.apache.lucene.index.DocumentsWriter$ResolveUpdatesEvent.process(DocumentsWriter.java:740)
>>>       at
>>> org.apache.lucene.index.IndexWriter.processEvents(IndexWriter.java:5106)
>>>       at
>>> org.apache.lucene.index.IndexWriter.processEvents(IndexWriter.java:5096)
>>>       at
>>>
>>> org.apache.lucene.index.IndexWriter.prepareCommitInternal(IndexWriter.java:3258)
>>>       at
>>> org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3458)
>>>       at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3423)
>>>       at
>>>
>>> org.apache.solr.update.DirectUpdateHandler2.closeWriter(DirectUpdateHandler2.java:875)
>>>       at
>>>
>>> org.apache.solr.update.DefaultSolrCoreState.closeIndexWriter(DefaultSolrCoreState.java:105)
>>>       at
>>>
>>> org.apache.solr.update.DefaultSolrCoreState.close(DefaultSolrCoreState.java:402)
>>>       at
>>>
>>> org.apache.solr.update.SolrCoreState.decrefSolrCoreState(SolrCoreState.java:83)
>>>       at org.apache.solr.core.SolrCore.close(SolrCore.java:1564)
>>>       at org.apache.solr.servlet.HttpSolrCall.destroy(HttpSolrCall.java:570)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:402)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:330)
>>>       at
>>>
>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
>>>       at
>>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:219)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:126)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at org.eclipse.jetty.server.Server.handle(Server.java:530)
>>>       at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347)
>>>       at
>>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256)
>>>       at
>>> org.eclipse.jetty.io
>>> .AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
>>>       at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102)
>>>       at org.eclipse.jetty.io
>>> .ChannelEndPoint$2.run(ChannelEndPoint.java:124)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:382)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626)
>>>       at java.lang.Thread.run(Thread.java:748)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.apache.lucene.index.BufferedUpdatesStream$ApplyDeletesResult
>>>       at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>       at
>>>
>>> org.eclipse.jetty.webapp.WebAppClassLoader.loadClass(WebAppClassLoader.java:565)
>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>       ... 50 more
>>> 2019-02-12 08:43:02.920 ERROR (qtp2137589296-19) [ x:COSBIBioIndex]
>>> o.a.s.c.SolrCore java.lang.NoClassDefFoundError:
>>> org/apache/solr/core/ShutdownAwareDirectory
>>>       at
>>>
>>> org.apache.solr.core.CachingDirectoryFactory.close(CachingDirectoryFactory.java:298)
>>>       at
>>>
>>> org.apache.solr.core.CachingDirectoryFactory.closeCacheValue(CachingDirectoryFactory.java:264)
>>>       at
>>>
>>> org.apache.solr.core.CachingDirectoryFactory.close(CachingDirectoryFactory.java:194)
>>>       at org.apache.solr.core.SolrCore.close(SolrCore.java:1633)
>>>       at org.apache.solr.servlet.HttpSolrCall.destroy(HttpSolrCall.java:570)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:402)
>>>       at
>>>
>>> org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:330)
>>>       at
>>>
>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1629)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
>>>       at
>>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
>>>       at
>>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
>>>       at
>>>
>>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:219)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:126)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at
>>>
>>> org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)
>>>       at
>>>
>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
>>>       at org.eclipse.jetty.server.Server.handle(Server.java:530)
>>>       at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347)
>>>       at
>>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256)
>>>       at
>>> org.eclipse.jetty.io
>>> .AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
>>>       at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102)
>>>       at org.eclipse.jetty.io
>>> .ChannelEndPoint$2.run(ChannelEndPoint.java:124)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:382)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708)
>>>       at
>>>
>>> org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626)
>>>       at java.lang.Thread.run(Thread.java:748)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.apache.solr.core.ShutdownAwareDirectory
>>>       at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>       at
>>>
>>> org.eclipse.jetty.webapp.WebAppClassLoader.loadClass(WebAppClassLoader.java:565)
>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>>>       ... 40 more
>>>
>>>
>>> --
>>> Danilo Tomasoni
>>> COSBI
>>>
>>> As for the European General Data Protection Regulation 2016/679 on the
>>> protection of natural persons with regard to the processing of personal
>>> data, we inform you that all the data we possess are object of treatement
>>> in the respect of the normative provided for by the cited GDPR.
>>>
>>> It is your right to be informed on which of your data are used and how;
>>> you may ask for their correction, cancellation or you may oppose to their
>>> use by written request sent by recorded delivery to The Microsoft Research
>>> – University of Trento Centre for Computational and Systems Biology Scarl,
>>> Piazza Manifattura 1, 38068 Rovereto (TN), Italy.
>>>
>>>
-- 
Danilo Tomasoni
COSBI

As for the European General Data Protection Regulation 2016/679 on the protection of natural
persons with regard to the processing of personal data, we inform you that all the data we
possess are object of treatement in the respect of the normative provided for by the cited
GDPR.

It is your right to be informed on which of your data are used and how; you may ask for their
correction, cancellation or you may oppose to their use by written request sent by recorded
delivery to The Microsoft Research – University of Trento Centre for Computational and Systems
Biology Scarl, Piazza Manifattura 1, 38068 Rovereto (TN), Italy.


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