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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/2019-05/">May, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-05-01T07:37:43+03:00">Wed May 01, 2019</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="2019-05-01">2019-05-01</h2>
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<ul>
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<li>Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace</li>
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<li>A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
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<ul>
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<li>Apparently if the item is in the <code>workflowitem</code> table it is submitted to a workflow</li>
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<li>And if it is in the <code>workspaceitem</code> table it is in the pre-submitted state</li>
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</ul>
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</li>
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<li>The item seems to be in a pre-submitted state, so I tried to delete it from there:</li>
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</ul>
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<pre><code>dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
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DELETE 1
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</code></pre><ul>
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<li>But after this I tried to delete the item from the XMLUI and it is <em>still</em> present…</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2019-05/'>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/2019-04/">April, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-04-01T09:00:43+03:00">Mon Apr 01, 2019</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="2019-04-01">2019-04-01</h2>
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<ul>
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<li>Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
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<ul>
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<li>They asked if we had plans to enable RDF support in CGSpace</li>
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</ul>
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</li>
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<li>There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
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<ul>
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<li>I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!</li>
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</ul>
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</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep 'Spore-192-EN-web.pdf' | grep -E '(18.196.196.108|18.195.78.144|18.195.218.6)' | awk '{print $9}' | sort | uniq -c | sort -n | tail -n 5
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4432 200
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</code></pre><ul>
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<li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li>
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<li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.country -m 228 -t ACTION -d
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$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -m 231 -t action -d
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$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d
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$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2019-04/'>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/2019-03/">March, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-03-01T12:16:30+01:00">Fri Mar 01, 2019</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="2019-03-01">2019-03-01</h2>
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<ul>
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<li>I checked IITA’s 259 Feb 14 records from last month for duplicates using Atmire’s Duplicate Checker on a fresh snapshot of CGSpace on my local machine and everything looks good</li>
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<li>I am now only waiting to hear from her about where the items should go, though I assume Journal Articles go to IITA Journal Articles collection, etc…</li>
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<li>Looking at the other half of Udana’s WLE records from 2018-11
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<ul>
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<li>I finished the ones for Restoring Degraded Landscapes (RDL), but these are for Variability, Risks and Competing Uses (VRC)</li>
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<li>I did the usual cleanups for whitespace, added regions where they made sense for certain countries, cleaned up the DOI link formats, added rights information based on the publications page for a few items</li>
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<li>Most worryingly, there are encoding errors in the abstracts for eleven items, for example:</li>
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<li>68.15% <20> 9.45 instead of 68.15% ± 9.45</li>
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<li>2003<EFBFBD>2013 instead of 2003–2013</li>
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</ul>
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</li>
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<li>I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2019-03/'>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/2019-02/">February, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-02-01T21:37:30+02:00">Fri Feb 01, 2019</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="2019-02-01">2019-02-01</h2>
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<ul>
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<li>Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!</li>
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<li>The top IPs before, during, and after this latest alert tonight were:</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 "01/Feb/2019:(17|18|19|20|21)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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245 207.46.13.5
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332 54.70.40.11
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385 5.143.231.38
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405 207.46.13.173
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405 207.46.13.75
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1117 66.249.66.219
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1121 35.237.175.180
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1546 5.9.6.51
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2474 45.5.186.2
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5490 85.25.237.71
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</code></pre><ul>
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<li><code>85.25.237.71</code> is the “Linguee Bot” that I first saw last month</li>
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<li>The Solr statistics the past few months have been very high and I was wondering if the web server logs also showed an increase</li>
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<li>There were just over 3 million accesses in the nginx logs last month:</li>
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</ul>
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<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2019"
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3018243
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real 0m19.873s
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user 0m22.203s
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sys 0m1.979s
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2019-02/'>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/2019-01/">January, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-01-02T09:48:30+02:00">Wed Jan 02, 2019</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="2019-01-02">2019-01-02</h2>
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<ul>
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<li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li>
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<li>I don’t see anything interesting in the web server logs around that time though:</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 "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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92 40.77.167.4
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99 210.7.29.100
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120 38.126.157.45
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177 35.237.175.180
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177 40.77.167.32
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216 66.249.75.219
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225 18.203.76.93
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261 46.101.86.248
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357 207.46.13.1
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903 54.70.40.11
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2019-01/'>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/2018-12/">December, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-12-02T02:09:30+02:00">Sun Dec 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="2018-12-01">2018-12-01</h2>
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<ul>
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<li>Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK</li>
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<li>I manually installed OpenJDK, then removed Oracle JDK, then re-ran the <a href="http://github.com/ilri/rmg-ansible-public">Ansible playbook</a> to update all configuration files, etc</li>
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<li>Then I ran all system updates and restarted the server</li>
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</ul>
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<h2 id="2018-12-02">2018-12-02</h2>
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<ul>
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<li>I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another <a href="https://usn.ubuntu.com/3831-1/">Ghostscript vulnerability last week</a></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-12/'>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/2018-11/">November, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 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="2018-11-01">2018-11-01</h2>
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<ul>
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<li>Finalize AReS Phase I and Phase II ToRs</li>
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<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
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</ul>
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<h2 id="2018-11-03">2018-11-03</h2>
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<ul>
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<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
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<li>Today these are the top 10 IPs:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>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/2018-10/">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>
|
||
<pre><code>[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
|
||
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
|
||
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
|
||
</code></pre><ul>
|
||
<li>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</li>
|
||
<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>
|
||
<li>I’m not sure why Tomcat didn’t crash with an OutOfMemoryError…</li>
|
||
<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>
|
||
<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>
|
||
<li>I ran all system updates on DSpace Test and rebooted it</li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-08/'>Read more →</a>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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