nav[aria-label="Primary Navigation"] { padding: 0; & ul { list-style: none; width: 100%; display: flex; flex-direction: row; justify-content: start; align-items: start; gap: 30px; padding: 0; & li { margin: 0; } & ul li { list-style: none; } } }

Unable to index Confluence after upgrading from 3.3.3 to 3.5.13

Jose Medina

I followed the instructions from the upgrade procedure

I backed up my index directory and created a new index directory and moved the plugin directory from the backup to the new index file and when I start confluence I see a lot of errors when confluence tries to index the attachments.

2017-01-04 08:53:15,955 WARN [Indexer: 1] [apache.pdfbox.util.PDFStreamEngine] processOperator java.io.IOException: Error: expected hex character and not  :32
 -- referer: https://mydomain.com/confluence/admin/search-indexes.action | url: /confluence/admin/reindex.action | userName: jmedina | action: reindex
java.io.IOException: Error: expected hex character and not  :32
        at org.apache.fontbox.cmap.CMapParser.parseNextToken(CMapParser.java:336)
        at org.apache.fontbox.cmap.CMapParser.parse(CMapParser.java:139)
        at org.apache.pdfbox.pdmodel.font.PDFont.parseCmap(PDFont.java:556)
        at org.apache.pdfbox.pdmodel.font.PDFont.encode(PDFont.java:390)
        at org.apache.pdfbox.util.PDFStreamEngine.processEncodedText(PDFStreamEngine.java:386)
        at org.apache.pdfbox.util.operator.ShowTextGlyph.process(ShowTextGlyph.java:61)
        at org.apache.pdfbox.util.PDFStreamEngine.processOperator(PDFStreamEngine.java:567)
        at org.apache.pdfbox.util.PDFStreamEngine.processSubStream(PDFStreamEngine.java:250)
        at org.apache.pdfbox.util.PDFStreamEngine.processStream(PDFStreamEngine.java:208)
        at org.apache.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:378)
        at org.apache.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:302)
        at org.apache.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:258)
        at com.atlassian.bonnie.search.extractor.PdfContentExtractor.extractText(PdfContentExtractor.java:50)
        at com.atlassian.bonnie.search.extractor.BaseAttachmentContentExtractor.addFields(BaseAttachmentContentExtractor.java:40)
        at com.atlassian.confluence.plugin.descriptor.ExtractorModuleDescriptor$BackwardsCompatibleExtractor.addFields(ExtractorModuleDescriptor.java:45)
        at com.atlassian.bonnie.search.BaseDocumentBuilder.getDocument(BaseDocumentBuilder.java:104)
        at com.atlassian.confluence.search.lucene.ConfluenceDocumentBuilder.getDocument(ConfluenceDocumentBuilder.java:97)
        at com.atlassian.confluence.search.lucene.tasks.AddDocumentIndexTask.perform(AddDocumentIndexTask.java:43)
        at com.atlassian.bonnie.index.TempIndexWriter.perform(TempIndexWriter.java:73)
        at com.atlassian.confluence.search.lucene.TempIndexWriterStrategy.perform(TempIndexWriterStrategy.java:43)
        at com.atlassian.confluence.search.lucene.tasks.TempIndexBackedIndexTaskPerformer.perform(TempIndexBackedIndexTaskPerformer.java:21)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker.indexCollection(DefaultObjectQueueWorker.java:104)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker$1.doInTransaction(DefaultObjectQueueWorker.java:71)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:127)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker.run(DefaultObjectQueueWorker.java:60)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1157)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:627)
        at java.lang.Thread.run(Thread.java:809)

2017-01-04 08:42:14,714 ERROR [Indexer: 1] [officeconnector.index.excel.ExcelXMLTextExtractor] endDocument expected [ 1646 ] entries but read [ 1670 ]
 -- referer: https://mydomain.com/confluence/admin/search-indexes.action | url: /confluence/admin/reindex.action | userName: jmedina | action: reindex
2017-01-04 08:42:14,720 WARN [Indexer: 5] [apache.pdfbox.util.PDFStreamEngine] processOperator java.lang.ClassCastException: org.apache.fontbox.cmap.CMapParser$Operator incompatible with [B
 -- referer: https://wikiclone.litle.com/confluence/admin/search-indexes.action | url: /confluence/admin/reindex.action | userName: jmedina | action: reindex
java.lang.ClassCastException: org.apache.fontbox.cmap.CMapParser$Operator incompatible with [B
        at org.apache.fontbox.cmap.CMapParser.parse(CMapParser.java:163)
        at org.apache.pdfbox.pdmodel.font.PDFont.parseCmap(PDFont.java:556)
        at org.apache.pdfbox.pdmodel.font.PDFont.encode(PDFont.java:390)
        at org.apache.pdfbox.util.PDFStreamEngine.processEncodedText(PDFStreamEngine.java:386)
        at org.apache.pdfbox.util.operator.ShowText.process(ShowText.java:45)
        at org.apache.pdfbox.util.PDFStreamEngine.processOperator(PDFStreamEngine.java:567)
        at org.apache.pdfbox.util.PDFStreamEngine.processSubStream(PDFStreamEngine.java:250)
        at org.apache.pdfbox.util.PDFStreamEngine.processStream(PDFStreamEngine.java:208)
        at org.apache.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:378)
        at org.apache.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:302)
        at org.apache.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:258)
        at com.atlassian.bonnie.search.extractor.PdfContentExtractor.extractText(PdfContentExtractor.java:50)
        at com.atlassian.bonnie.search.extractor.BaseAttachmentContentExtractor.addFields(BaseAttachmentContentExtractor.java:40)
        at com.atlassian.confluence.plugin.descriptor.ExtractorModuleDescriptor$BackwardsCompatibleExtractor.addFields(ExtractorModuleDescriptor.java:45)
        at com.atlassian.bonnie.search.BaseDocumentBuilder.getDocument(BaseDocumentBuilder.java:104)
        at com.atlassian.confluence.search.lucene.ConfluenceDocumentBuilder.getDocument(ConfluenceDocumentBuilder.java:97)
        at com.atlassian.confluence.search.lucene.tasks.AddDocumentIndexTask.perform(AddDocumentIndexTask.java:43)
        at com.atlassian.bonnie.index.TempIndexWriter.perform(TempIndexWriter.java:73)
        at com.atlassian.confluence.search.lucene.TempIndexWriterStrategy.perform(TempIndexWriterStrategy.java:43)
        at com.atlassian.confluence.search.lucene.tasks.TempIndexBackedIndexTaskPerformer.perform(TempIndexBackedIndexTaskPerformer.java:21)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker.indexCollection(DefaultObjectQueueWorker.java:104)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker$1.doInTransaction(DefaultObjectQueueWorker.java:71)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:127)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker.run(DefaultObjectQueueWorker.java:60)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1157)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:627)
        at java.lang.Thread.run(Thread.java:809)

2017-01-04 09:03:52,413 ERROR [Indexer: 2] [officeconnector.index.excel.ExcelXMLTextExtractor] endDocument expected [ 3736 ] entries but read [ 3767 ]
 -- referer: https://mydomain.com/confluence/admin/search-indexes.action | url: /confluence/admin/reindex.action | userName: jmedina | action: reindex
2017-01-04 09:04:01,864 ERROR [Indexer: 6] [confluence.search.lucene.DefaultObjectQueueWorker] indexCollection Error indexing document
 -- referer: https://mydomain.com/confluence/admin/search-indexes.action | url: /confluence/admin/reindex.action | userName: jmedina | action: reindex
java.lang.OutOfMemoryError: Java heap space
        at java.lang.StringBuilder.ensureCapacityImpl(StringBuilder.java:342)
        at java.lang.StringBuilder.append(StringBuilder.java:208)
        at com.atlassian.confluence.extra.officeconnector.index.excel.ExcelXMLTextExtractor$PartHandler.appendToOutput(ExcelXMLTextExtractor.java:195)
        at com.atlassian.confluence.extra.officeconnector.index.excel.ExcelXMLTextExtractor$PartHandler.endElement(ExcelXMLTextExtractor.java:185)
        at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(Unknown Source)
        at com.atlassian.confluence.extra.officeconnector.index.excel.ExcelXMLTextExtractor.parseEntry(ExcelXMLTextExtractor.java:123)
        at com.atlassian.confluence.extra.officeconnector.index.excel.ExcelXMLTextExtractor.extractText(ExcelXMLTextExtractor.java:83)
        at com.atlassian.bonnie.search.extractor.BaseAttachmentContentExtractor.addFields(BaseAttachmentContentExtractor.java:40)
        at com.atlassian.confluence.plugin.descriptor.ExtractorModuleDescriptor$BackwardsCompatibleExtractor.addFields(ExtractorModuleDescriptor.java:45)
        at com.atlassian.bonnie.search.BaseDocumentBuilder.getDocument(BaseDocumentBuilder.java:104)
        at com.atlassian.confluence.search.lucene.ConfluenceDocumentBuilder.getDocument(ConfluenceDocumentBuilder.java:97)
        at com.atlassian.confluence.search.lucene.tasks.AddDocumentIndexTask.perform(AddDocumentIndexTask.java:43)
        at com.atlassian.bonnie.index.TempIndexWriter.perform(TempIndexWriter.java:73)
        at com.atlassian.confluence.search.lucene.TempIndexWriterStrategy.perform(TempIndexWriterStrategy.java:43)
        at com.atlassian.confluence.search.lucene.tasks.TempIndexBackedIndexTaskPerformer.perform(TempIndexBackedIndexTaskPerformer.java:21)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker.indexCollection(DefaultObjectQueueWorker.java:104)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker$1.doInTransaction(DefaultObjectQueueWorker.java:71)
        at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:127)
        at com.atlassian.confluence.search.lucene.DefaultObjectQueueWorker.run(DefaultObjectQueueWorker.java:60)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1157)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:627)
        at java.lang.Thread.run(Thread.java:809)

Accepted answers

All comments

Nic Brough -Adaptavist-

There are two errors here

One is that your attachments can't be read by Confluence. This is usually because the files are in a newer format than the libraries Confluence uses for reading them can cope with. Confluence 3 is very very old and won't be aware of attachment formats that have been adopted in the last six years.

These errors simply mean the attachment content can't be indexed, and hence can't be searched.

The second is a bit more of a pain. It's run out of memory while trying to read one of the docs. This might be anything, but it could be that the errors while trying to index files it can't read are causing some loss of memory. You could do a more detailed analysis of what is chewing up all the memory, or just chuck more memory at it and hope it improves (not a great idea in most cases).

But I'd be most tempted to disable the attachment indexing - go to admin -> add-ons, and select the "system" types and find the attachments extractor and office connector add-ons. Within them, turn off the modules that are throwing the conversion errors - pdf and excel at a glance.

Jose Medina

Thanks for the recommendation,

I'm trying to upgrade to 6 from 3 and i'm following the upgrade path upgrading to 3.5 and then to 5.0 and then to 6. I was wondering if I can continue to upgrade process without indexing the content until I get to the latest version.

Nic Brough -Adaptavist-

Ah, good. Yes, if you turn off the indexing of the attachments, you won't lose anything other than the ability to search the current version, which you don't care about because you're going to upgrade. You can re-enable it when you reach the target version, and run a full re-index. I'd expect a lot fewer "can't read attachment" errors then smile

Jose Medina

Are there any downside if I start on a new data folder and only copy the confluence.cfg.conf file and I upgrade confluence to 3.5.,5.0.13 and then to 6.0.2?

I had been messing with that setup and I saw when it was doing the index it failed to locate the attachments which was obvious because I didn't have anything on the data folder.

Welcome!

It looks like you're new here. Sign in or register to get started.

Quick Links

Find more posts tagged with

confluence

confluence-administration