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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-10/">October, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-10-01T22:31:54+03:00">Mon Oct 01, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-10-01">2018-10-01</h2>
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<ul>
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<li>Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items</li>
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<li>I created a GitHub issue to track this <a href="https://github.com/ilri/DSpace/issues/389">#389</a>, because I’m super busy in Nairobi right now</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-10/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-09/">September, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-09-02T09:55:54+03:00">Sun Sep 02, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-09-02">2018-09-02</h2>
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<ul>
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<li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li>
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<li>I’ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
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<li>Also, I’ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
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<li>I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-09/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-08/">August, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-08-01">2018-08-01</h2>
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<ul>
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<li>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</li>
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</ul>
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<pre tabindex="0"><code>[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
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[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
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[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
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</code></pre><ul>
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<li>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</li>
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<li>From the DSpace log I see that eventually Solr stopped responding, so I guess the <code>java</code> process that was OOM killed above was Tomcat’s</li>
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<li>I’m not sure why Tomcat didn’t crash with an OutOfMemoryError…</li>
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<li>Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core</li>
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<li>The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes</li>
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<li>I ran all system updates on DSpace Test and rebooted it</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-08/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-07-01T12:56:54+03:00">Sun Jul 01, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-07-01">2018-07-01</h2>
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<ul>
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<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
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</ul>
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<pre tabindex="0"><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
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</code></pre><ul>
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<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
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</ul>
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<pre tabindex="0"><code>There is insufficient memory for the Java Runtime Environment to continue.
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2018-07/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-06/">June, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-06-04T19:49:54-07:00">Mon Jun 04, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-06-04">2018-06-04</h2>
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<ul>
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<li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>)
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<ul>
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<li>There seems to be a problem with the CUA and L&R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn’t build</li>
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</ul>
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</li>
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<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
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<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
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</ul>
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<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
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</code></pre><ul>
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<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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<li>Time to index ~70,000 items on CGSpace:</li>
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</ul>
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<pre tabindex="0"><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
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real 74m42.646s
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user 8m5.056s
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sys 2m7.289s
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2018-06/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-05/">May, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-05-01T16:43:54+03:00">Tue May 01, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-05-01">2018-05-01</h2>
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<ul>
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<li>I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
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<ul>
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<li>http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E</li>
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<li>http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E</li>
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</ul>
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</li>
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<li>Then I reduced the JVM heap size from 6144 back to 5120m</li>
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<li>Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to support hosts choosing which distribution they want to use</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-05/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><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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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category 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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<a href='https://alanorth.github.io/cgspace-notes/2018-04/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-03/">March, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-03-02T16:07:54+02:00">Fri Mar 02, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-03-02">2018-03-02</h2>
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<ul>
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<li>Export a CSV of the IITA community metadata for Martin Mueller</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-03/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-02/">February, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-02-01T16:28:54+02:00">Thu Feb 01, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-02-01">2018-02-01</h2>
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<ul>
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<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
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<li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li>
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<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
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<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu’s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-02/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-01-02">2018-01-02</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
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<li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li>
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<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
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<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
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<li>And just before that I see this:</li>
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</ul>
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<pre tabindex="0"><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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</code></pre><ul>
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<li>Ah hah! So the pool was actually empty!</li>
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<li>I need to increase that, let’s try to bump it up from 50 to 75</li>
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<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</li>
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<li>I notice this error quite a few times in dspace.log:</li>
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</ul>
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<pre tabindex="0"><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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</code></pre><ul>
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<li>And there are many of these errors every day for the past month:</li>
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</ul>
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<pre tabindex="0"><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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</code></pre><ul>
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<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
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