com.atlassian.jira.issue.index.IndexException

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  • A user reported getting errors when transitioning an issue: Errors * com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF In the logs, this "read past EOF" error first occurs when the nightly reindex runs: 2007-01-28 00:00:00,019 JiraQuartzScheduler_Worker-0 INFO [issue.index.job.OptimizeIndexJob] Optimize Index Job running... 2007-01-28 00:00:00,341 JiraQuartzScheduler_Worker-0 ERROR [issue.index.job.OptimizeIndexJob] Error occurred while optimizing indexes. com.atlassian.jira.issue.index.IndexException: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.jira.issue.index.DefaultIndexManager.optimize(DefaultIndexManager.java:374) at com.atlassian.jira.issue.index.job.OptimizeIndexJob.execute(OptimizeIndexJob.java:19) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) Caused by: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.bonnie.ConcurrentLuceneConnection.withWriter(ConcurrentLuceneConnection.java:303) at com.atlassian.bonnie.ConcurrentLuceneConnection.optimize(ConcurrentLuceneConnection.java:116) at com.atlassian.jira.issue.index.SingleThreadedIssueIndexer.optimize(SingleThreadedIssueIndexer.java:74) at com.atlassian.jira.issue.index.DefaultIndexManager.optimize0(DefaultIndexManager.java:393) at com.atlassian.jira.issue.index.DefaultIndexManager.optimize(DefaultIndexManager.java:370) ... 3 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:60) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:33) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:46) at org.apache.lucene.index.SegmentTermEnum.<init>(SegmentTermEnum.java:47) at org.apache.lucene.index.TermInfosReader.<init>(TermInfosReader.java:52) at org.apache.lucene.index.SegmentReader.initialize(SegmentReader.java:147) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:129) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:110) at org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:674) at org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:658) at org.apache.lucene.index.IndexWriter.optimize(IndexWriter.java:517) at com.atlassian.bonnie.ConcurrentLuceneConnection$2.perform(ConcurrentLuceneConnection.java:120) at com.atlassian.bonnie.ConcurrentLuceneConnection.withWriter(ConcurrentLuceneConnection.java:296) ... 7 more It seems that after this, the index is corrupt and any further attempt to modify it results in an error: 2007-01-28 00:29:19,998 TP-Processor294 ERROR [event.listeners.search.IssueIndexListener] Error re-indexing Issue[GenericEntity:Issue][summary,cloneNode forgets IDness of attribute][status,1][votes,0][fixfor,null][assignee,null][security,null][resolution,null][type,1][timespent,null][id,27912][reporter,elharo@metalab.unc.edu][project,10520][environment,java version "1.4.2_05" Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_05-141.3) Java HotSpot(TM) Client VM (build 1.4.2-38, mixed mode)][component,null][updated,2007-01-28 00:29:19.917][created,2004-10-22 06:24:43.0][workflowId,37907][description,Cloning a node that contains an ID type attribute forgets that the attribute is an ID. Interestingly importing the element into a new document, even one without a DocType, does not forget that the Attr has ID type. The attached program generates the following output: Xerces-J 2.6.2 Found element with ID Did not find element with ID][priority,3][timeestimate,null][duedate,null][timeoriginalestimate,null][key,XERCESJ-1022] com.atlassian.jira.issue.index.IndexException: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:292) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:244) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:264) at com.atlassian.jira.event.listeners.search.IssueIndexListener.reIndex(IssueIndexListener.java:109) at com.atlassian.jira.event.listeners.search.IssueIndexListener.reIndex(IssueIndexListener.java:119) at com.atlassian.jira.event.listeners.search.IssueIndexListener.issueCommented(IssueIndexListener.java:75) at com.atlassian.jira.event.issue.AbstractIssueEventListener.workflowEvent(AbstractIssueEventListener.java:106) at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(IssueEventDispatcher.java:107) at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(IssueEventDispatcher.java:82) at com.atlassian.jira.web.action.issue.AddComment.alertSystemOfComment(AddComment.java:101) at com.atlassian.jira.web.action.issue.AddComment.doExecute(AddComment.java:85) at webwork.action.ActionSupport.execute(ActionSupport.java:153) at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:54) ...... at java.lang.Thread.run(Thread.java:619) Caused by: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.bonnie.ConcurrentLuceneConnection.constructIndexDeleter(ConcurrentLuceneConnection.java:438) at com.atlassian.bonnie.ConcurrentLuceneConnection.withReaderAndDeletes(ConcurrentLuceneConnection.java:261) at com.atlassian.bonnie.ConcurrentLuceneConnection.withDeleteAndWrites(ConcurrentLuceneConnection.java:324) at com.atlassian.jira.issue.index.SingleThreadedIssueIndexer.reindexIssues(SingleThreadedIssueIndexer.java:332) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:287) ... 68 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:60) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:33) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:46) at org.apache.lucene.index.SegmentTermEnum.<init>(SegmentTermEnum.java:47) at org.apache.lucene.index.TermInfosReader.<init>(TermInfosReader.java:52) at org.apache.lucene.index.SegmentReader.initialize(SegmentReader.java:147) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:129) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:110) at org.apache.lucene.index.IndexReader$1.doBody(IndexReader.java:154) at org.apache.lucene.store.Lock$With.run(Lock.java:109) at org.apache.lucene.index.IndexReader.open(IndexReader.java:143) at org.apache.lucene.index.IndexReader.open(IndexReader.java:138) at com.atlassian.bonnie.ConcurrentLuceneConnection.constructIndexDeleter(ConcurrentLuceneConnection.java:434) ... 72 more
    via by Jeff Turner,
  • A user reported getting errors when transitioning an issue: Errors * com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF In the logs, this "read past EOF" error first occurs when the nightly reindex runs: 2007-01-28 00:00:00,019 JiraQuartzScheduler_Worker-0 INFO [issue.index.job.OptimizeIndexJob] Optimize Index Job running... 2007-01-28 00:00:00,341 JiraQuartzScheduler_Worker-0 ERROR [issue.index.job.OptimizeIndexJob] Error occurred while optimizing indexes. com.atlassian.jira.issue.index.IndexException: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.jira.issue.index.DefaultIndexManager.optimize(DefaultIndexManager.java:374) at com.atlassian.jira.issue.index.job.OptimizeIndexJob.execute(OptimizeIndexJob.java:19) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) Caused by: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.bonnie.ConcurrentLuceneConnection.withWriter(ConcurrentLuceneConnection.java:303) at com.atlassian.bonnie.ConcurrentLuceneConnection.optimize(ConcurrentLuceneConnection.java:116) at com.atlassian.jira.issue.index.SingleThreadedIssueIndexer.optimize(SingleThreadedIssueIndexer.java:74) at com.atlassian.jira.issue.index.DefaultIndexManager.optimize0(DefaultIndexManager.java:393) at com.atlassian.jira.issue.index.DefaultIndexManager.optimize(DefaultIndexManager.java:370) ... 3 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:60) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:33) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:46) at org.apache.lucene.index.SegmentTermEnum.<init>(SegmentTermEnum.java:47) at org.apache.lucene.index.TermInfosReader.<init>(TermInfosReader.java:52) at org.apache.lucene.index.SegmentReader.initialize(SegmentReader.java:147) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:129) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:110) at org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:674) at org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:658) at org.apache.lucene.index.IndexWriter.optimize(IndexWriter.java:517) at com.atlassian.bonnie.ConcurrentLuceneConnection$2.perform(ConcurrentLuceneConnection.java:120) at com.atlassian.bonnie.ConcurrentLuceneConnection.withWriter(ConcurrentLuceneConnection.java:296) ... 7 more It seems that after this, the index is corrupt and any further attempt to modify it results in an error: 2007-01-28 00:29:19,998 TP-Processor294 ERROR [event.listeners.search.IssueIndexListener] Error re-indexing Issue[GenericEntity:Issue][summary,cloneNode forgets IDness of attribute][status,1][votes,0][fixfor,null][assignee,null][security,null][resolution,null][type,1][timespent,null][id,27912][reporter,elharo@metalab.unc.edu][project,10520][environment,java version "1.4.2_05" Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_05-141.3) Java HotSpot(TM) Client VM (build 1.4.2-38, mixed mode)][component,null][updated,2007-01-28 00:29:19.917][created,2004-10-22 06:24:43.0][workflowId,37907][description,Cloning a node that contains an ID type attribute forgets that the attribute is an ID. Interestingly importing the element into a new document, even one without a DocType, does not forget that the Attr has ID type. The attached program generates the following output: Xerces-J 2.6.2 Found element with ID Did not find element with ID][priority,3][timeestimate,null][duedate,null][timeoriginalestimate,null][key,XERCESJ-1022] com.atlassian.jira.issue.index.IndexException: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:292) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:244) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndex(DefaultIndexManager.java:264) at com.atlassian.jira.event.listeners.search.IssueIndexListener.reIndex(IssueIndexListener.java:109) at com.atlassian.jira.event.listeners.search.IssueIndexListener.reIndex(IssueIndexListener.java:119) at com.atlassian.jira.event.listeners.search.IssueIndexListener.issueCommented(IssueIndexListener.java:75) at com.atlassian.jira.event.issue.AbstractIssueEventListener.workflowEvent(AbstractIssueEventListener.java:106) at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(IssueEventDispatcher.java:107) at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(IssueEventDispatcher.java:82) at com.atlassian.jira.web.action.issue.AddComment.alertSystemOfComment(AddComment.java:101) at com.atlassian.jira.web.action.issue.AddComment.doExecute(AddComment.java:85) at webwork.action.ActionSupport.execute(ActionSupport.java:153) at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:54) ...... at java.lang.Thread.run(Thread.java:619) Caused by: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.bonnie.ConcurrentLuceneConnection.constructIndexDeleter(ConcurrentLuceneConnection.java:438) at com.atlassian.bonnie.ConcurrentLuceneConnection.withReaderAndDeletes(ConcurrentLuceneConnection.java:261) at com.atlassian.bonnie.ConcurrentLuceneConnection.withDeleteAndWrites(ConcurrentLuceneConnection.java:324) at com.atlassian.jira.issue.index.SingleThreadedIssueIndexer.reindexIssues(SingleThreadedIssueIndexer.java:332) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:287) ... 68 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:60) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:33) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:46) at org.apache.lucene.index.SegmentTermEnum.<init>(SegmentTermEnum.java:47) at org.apache.lucene.index.TermInfosReader.<init>(TermInfosReader.java:52) at org.apache.lucene.index.SegmentReader.initialize(SegmentReader.java:147) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:129) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:110) at org.apache.lucene.index.IndexReader$1.doBody(IndexReader.java:154) at org.apache.lucene.store.Lock$With.run(Lock.java:109) at org.apache.lucene.index.IndexReader.open(IndexReader.java:143) at org.apache.lucene.index.IndexReader.open(IndexReader.java:138) at com.atlassian.bonnie.ConcurrentLuceneConnection.constructIndexDeleter(ConcurrentLuceneConnection.java:434) ... 72 more
    via by Jeff Turner,
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    via by Unknown author,
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    • com.atlassian.jira.issue.index.IndexException: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.jira.issue.index.DefaultIndexManager.optimize(DefaultIndexManager.java:374) at com.atlassian.jira.issue.index.job.OptimizeIndexJob.execute(OptimizeIndexJob.java:19) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) Caused by: com.atlassian.bonnie.LuceneException: java.io.IOException: read past EOF at com.atlassian.bonnie.ConcurrentLuceneConnection.withWriter(ConcurrentLuceneConnection.java:303) at com.atlassian.bonnie.ConcurrentLuceneConnection.optimize(ConcurrentLuceneConnection.java:116) at com.atlassian.jira.issue.index.SingleThreadedIssueIndexer.optimize(SingleThreadedIssueIndexer.java:74) at com.atlassian.jira.issue.index.DefaultIndexManager.optimize0(DefaultIndexManager.java:393) at com.atlassian.jira.issue.index.DefaultIndexManager.optimize(DefaultIndexManager.java:370) ... 3 more Caused by: java.io.IOException: read past EOF at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:60) at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:33) at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:46) at org.apache.lucene.index.SegmentTermEnum.<init>(SegmentTermEnum.java:47) at org.apache.lucene.index.TermInfosReader.<init>(TermInfosReader.java:52) at org.apache.lucene.index.SegmentReader.initialize(SegmentReader.java:147) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:129) at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:110) at org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:674) at org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:658) at org.apache.lucene.index.IndexWriter.optimize(IndexWriter.java:517) at com.atlassian.bonnie.ConcurrentLuceneConnection$2.perform(ConcurrentLuceneConnection.java:120) at com.atlassian.bonnie.ConcurrentLuceneConnection.withWriter(ConcurrentLuceneConnection.java:296) ... 7 more

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