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I tried to test something on DSpace Test but noticed that it’s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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I tried to test something on DSpace Test but noticed that it’s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-04/">April, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-04-01T16:13:54+02:00">Sun Apr 01, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-04-01">2018-04-01</h2>
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<ul>
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<li>I tried to test something on DSpace Test but noticed that it’s down since god knows when</li>
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<li>Catalina logs at least show some memory errors yesterday:</li>
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</ul>
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<p></p>
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<pre><code>Mar 31, 2018 10:26:42 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
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SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
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java.lang.OutOfMemoryError: Java heap space
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Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>So this is getting super annoying</li>
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<li>I ran all system updates on DSpace Test and rebooted it</li>
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<li>For some reason Listings and Reports is not giving any results for any queries now…</li>
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<li>I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module</li>
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<li>Help Lili Szilagyi with a question about statistics on some CCAFS items</li>
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</ul>
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<h2 id="2018-04-04">2018-04-04</h2>
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<ul>
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<li>Peter noticed that there were still some old CRP names on CGSpace, because I hadn’t forced the Discovery index to be updated after I fixed the others last week</li>
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<li>For completeness I re-ran the CRP corrections on CGSpace:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
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Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
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</code></pre>
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<ul>
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<li>Then started a full Discovery index:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 76m13.841s
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user 8m22.960s
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sys 2m2.498s
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</code></pre>
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<ul>
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<li>Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme’s items</li>
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<li>I used my <a href="https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py">add-orcid-identifiers-csv.py</a> script:</li>
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</ul>
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<pre><code>$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>The CSV format of <code>jtohme-2018-04-04.csv</code> was:</li>
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</ul>
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<pre><code class="language-csv">dc.contributor.author,cg.creator.id
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"Tohme, Joseph M.",Joe Tohme: 0000-0003-2765-7101
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</code></pre>
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<ul>
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<li>There was a quoting error in my CRP CSV and the replacements for <code>Forests, Trees and Agroforestry</code> got messed up</li>
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<li>So I fixed them and had to re-index again!</li>
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<li>I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:</li>
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</ul>
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<pre><code>$ git checkout -b 5_x-dspace-5.8 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.8
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</code></pre>
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<ul>
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<li>I was prepared to skip some commits that I had cherry picked from the upstream <code>dspace-5_x</code> branch when we did the DSpace 5.5 upgrade (see notes on 2016-10-19 and 2017-12-17):
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<ul>
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<li>[DS-3246] Improve cleanup in recyclable components (upstream commit on dspace-5_x: 9f0f5940e7921765c6a22e85337331656b18a403)</li>
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<li>[DS-3250] applying patch provided by Atmire (upstream commit on dspace-5_x: c6fda557f731dbc200d7d58b8b61563f86fe6d06)</li>
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<li>bump up to latest minor pdfbox version (upstream commit on dspace-5_x: b5330b78153b2052ed3dc2fd65917ccdbfcc0439)</li>
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<li>DS-3583 Usage of correct Collection Array (#1731) (upstream commit on dspace-5_x: c8f62e6f496fa86846bfa6bcf2d16811087d9761)</li>
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</ul></li>
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<li>… but somehow git knew, and didn’t include them in my interactive rebase!</li>
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<li>I need to send this branch to Atmire and also arrange payment (see <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">ticket #560</a> in their tracker)</li>
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<li>Fix Sisay’s SSH access to the new DSpace Test server (linode19)</li>
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</ul>
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<h2 id="2018-04-05">2018-04-05</h2>
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<ul>
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<li>Fix Sisay’s sudo access on the new DSpace Test server (linode19)</li>
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<li>The reindexing process on DSpace Test took <em>forever</em> yesterday:</li>
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</ul>
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<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 599m32.961s
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user 9m3.947s
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sys 2m52.585s
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</code></pre>
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<ul>
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<li>So we really should not use this Linode block storage for Solr</li>
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<li>Assetstore might be fine but would complicate things with configuration and deployment (ughhh)</li>
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<li>Better to use Linode block storage only for backup</li>
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<li>Help Peter with the GDPR compliance / reporting form for CGSpace</li>
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<li>DSpace Test crashed due to memory issues again:</li>
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</ul>
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<pre><code># grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
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16
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</code></pre>
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<ul>
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<li>I ran all system updates on DSpace Test and rebooted it</li>
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<li>Proof some records on DSpace Test for Udana from IWMI</li>
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<li>He has done better with the small syntax and consistency issues but then there are larger concerns with not linking to DOIs, copying titles incorrectly, etc</li>
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</ul>
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<h2 id="2018-04-10">2018-04-10</h2>
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<ul>
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<li>I got a notice that CGSpace CPU usage was very high this morning</li>
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<li>Looking at the nginx logs, here are the top users today so far:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "10/Apr/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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282 207.46.13.112
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286 54.175.208.220
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287 207.46.13.113
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298 66.249.66.153
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322 207.46.13.114
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780 104.196.152.243
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3994 178.154.200.38
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4295 70.32.83.92
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4388 95.108.181.88
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7653 45.5.186.2
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</code></pre>
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<ul>
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<li>45.5.186.2 is of course CIAT</li>
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<li>95.108.181.88 appears to be Yandex:</li>
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</ul>
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<pre><code>95.108.181.88 - - [09/Apr/2018:06:34:16 +0000] "GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1" 200 2638 "-" "Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)"
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</code></pre>
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<ul>
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<li>And for some reason Yandex created a lot of Tomcat sessions today:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88' dspace.log.2018-04-10
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4363
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</code></pre>
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<ul>
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<li>70.32.83.92 appears to be some harvester we’ve seen before, but on a new IP</li>
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<li>They are not creating new Tomcat sessions so there is no problem there</li>
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<li>178.154.200.38 also appears to be Yandex, and is also creating many Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=178.154.200.38' dspace.log.2018-04-10
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3982
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</code></pre>
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<ul>
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<li>I’m not sure why Yandex creates so many Tomcat sessions, as its user agent should match the Crawler Session Manager valve</li>
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<li>Let’s try a manual request with and without their user agent:</li>
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</ul>
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<pre><code>$ http --print Hh https://cgspace.cgiar.org/bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg 'User-Agent:Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)'
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GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1
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Accept: */*
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Accept-Encoding: gzip, deflate
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Connection: keep-alive
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Host: cgspace.cgiar.org
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User-Agent: Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)
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HTTP/1.1 200 OK
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Connection: keep-alive
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Content-Language: en-US
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Content-Length: 2638
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Content-Type: image/jpeg;charset=ISO-8859-1
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Date: Tue, 10 Apr 2018 05:18:37 GMT
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Expires: Tue, 10 Apr 2018 06:18:37 GMT
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Last-Modified: Tue, 25 Apr 2017 07:05:54 GMT
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Server: nginx
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Strict-Transport-Security: max-age=15768000
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Vary: User-Agent
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X-Cocoon-Version: 2.2.0
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X-Content-Type-Options: nosniff
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X-Frame-Options: SAMEORIGIN
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X-XSS-Protection: 1; mode=block
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$ http --print Hh https://cgspace.cgiar.org/bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg
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GET /bitstream/handle/10568/21794/ILRI_logo_usage.jpg.jpg HTTP/1.1
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Accept: */*
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Accept-Encoding: gzip, deflate
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Connection: keep-alive
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Host: cgspace.cgiar.org
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User-Agent: HTTPie/0.9.9
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HTTP/1.1 200 OK
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Connection: keep-alive
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Content-Language: en-US
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Content-Length: 2638
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Content-Type: image/jpeg;charset=ISO-8859-1
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Date: Tue, 10 Apr 2018 05:20:08 GMT
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Expires: Tue, 10 Apr 2018 06:20:08 GMT
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Last-Modified: Tue, 25 Apr 2017 07:05:54 GMT
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Server: nginx
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Set-Cookie: JSESSIONID=31635DB42B66D6A4208CFCC96DD96875; Path=/; Secure; HttpOnly
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Strict-Transport-Security: max-age=15768000
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Vary: User-Agent
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X-Cocoon-Version: 2.2.0
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X-Content-Type-Options: nosniff
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X-Frame-Options: SAMEORIGIN
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X-XSS-Protection: 1; mode=block
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</code></pre>
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<ul>
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<li>So it definitely looks like Yandex requests are getting assigned a session from the Crawler Session Manager valve</li>
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<li>And if I look at the DSpace log I see its IP sharing a session with other crawlers like Google (66.249.66.153)</li>
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<li>Indeed the number of Tomcat sessions appears to be normal:</li>
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</ul>
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<p><img src="/cgspace-notes/2018/04/jmx_dspace_sessions-week.png" alt="Tomcat sessions week" /></p>
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<ul>
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<li>In other news, it looks like the number of total requests processed by nginx in March went down from the previous months:</li>
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</ul>
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<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Mar/2018"
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2266594
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real 0m13.658s
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user 0m16.533s
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sys 0m1.087s
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</code></pre>
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<ul>
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<li>In other other news, the database cleanup script has an issue again:</li>
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</ul>
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<pre><code>$ dspace cleanup -v
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...
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Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
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Detail: Key (bitstream_id)=(151626) is still referenced from table "bundle".
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</code></pre>
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<ul>
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<li>The solution is, as always:</li>
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</ul>
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<pre><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (151626);'
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UPDATE 1
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</code></pre>
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<ul>
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<li>Looking at abandoned connections in Tomcat:</li>
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</ul>
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<pre><code># zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
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2115
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</code></pre>
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<ul>
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<li>Apparently from these stacktraces we should be able to see which code is not closing connections properly</li>
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<li>Here’s a pretty good overview of days where we had database issues recently:</li>
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</ul>
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<pre><code># zcat /var/log/tomcat7/catalina.out.[1-9].gz | grep 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon' | awk '{print $1,$2, $3}' | sort | uniq -c | sort -n
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1 Feb 18, 2018
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1 Feb 19, 2018
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1 Feb 20, 2018
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1 Feb 24, 2018
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2 Feb 13, 2018
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3 Feb 17, 2018
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5 Feb 16, 2018
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5 Feb 23, 2018
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5 Feb 27, 2018
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6 Feb 25, 2018
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40 Feb 14, 2018
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63 Feb 28, 2018
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154 Mar 19, 2018
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202 Feb 21, 2018
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264 Feb 26, 2018
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268 Mar 21, 2018
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524 Feb 22, 2018
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570 Feb 15, 2018
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</code></pre>
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<ul>
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<li>In Tomcat 8.5 the <code>removeAbandoned</code> property has been split into two: <code>removeAbandonedOnBorrow</code> and <code>removeAbandonedOnMaintenance</code></li>
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<li>See: <a href="https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations">https://tomcat.apache.org/tomcat-8.5-doc/jndi-datasource-examples-howto.html#Database_Connection_Pool_(DBCP_2)_Configurations</a></li>
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<li>I assume we want <code>removeAbandonedOnBorrow</code> and make updates to the Tomcat 8 templates in Ansible</li>
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<li>After reading more documentation I see that Tomcat 8.5’s default DBCP seems to now be Commons DBCP2 instead of Tomcat DBCP</li>
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<li>It can be overridden in Tomcat’s <em>server.xml</em> by setting <code>factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"</code> in the <code><Resource></code></li>
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<li>I think we should use this default, so we’ll need to remove some other settings that are specific to Tomcat’s DBCP like <code>jdbcInterceptors</code> and <code>abandonWhenPercentageFull</code></li>
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</ul>
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2018-04/">April, 2018</a></li>
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<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
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<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
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<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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</p>
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<p>
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<a href="#">Back to top</a>
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