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https://issues.apache.org/jira/browse/NUTCH-1113?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13867945#comment-13867945
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Markus Jelsma commented on NUTCH-1113:
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I have two narrowed the problem down to a single URL and two segments from 
production. The first is a fetch_success and the second is linked. Merging this 
on trunk results in linked, not fetch_success! For some strange reason, i could 
not reproduce this in a controlled environment, my local mode, so no unit test 
that picks this up, although it is almost identical to the mostlyLinks unit 
test.

To finally get a quick win i decided to ignore linked crawl datums completely! 
This significantly reduces segments size but also seems to finally give me 
reliable results when indexing. 

> Merging segments causes URLs to vanish from crawldb/index?
> ----------------------------------------------------------
>
>                 Key: NUTCH-1113
>                 URL: https://issues.apache.org/jira/browse/NUTCH-1113
>             Project: Nutch
>          Issue Type: Bug
>    Affects Versions: 1.3
>            Reporter: Edward Drapkin
>            Priority: Blocker
>             Fix For: 1.9
>
>         Attachments: NUTCH-1113-junit.patch, NUTCH-1113-junit.patch, 
> NUTCH-1113-junit.patch, NUTCH-1113-junit.patch, NUTCH-1113-trunk.patch, 
> merged_segment_output.txt, unmerged_segment_output.txt
>
>
> When I run Nutch, I use the following steps:
> nutch inject crawldb/ url.txt
> repeated 3 times:
> nutch generate crawldb/ segments/ -normalize
> nutch fetch `ls -d segments/* | tail -1`
> nutch parse `ls -d segments/* | tail -1`
> nutch update crawldb `ls -d segments/* | tail -1`
> nutch mergesegs merged/ -dir segments/
> nutch invertlinks linkdb/ -dir merged/
> nutch index index/ crawldb/ linkdb/ -dir merged/ (I forward ported the lucene 
> indexing code from Nutch 1.1).
> When I crawl with merging segments, I lose about 20% of the URLs that wind up 
> in the index vs. when I crawl without merging the segments.  Somehow the 
> segment merger causes me to lose ~20% of my crawl database!



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