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<meta property="og:description" content="2018-10-01 Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now 2018-10-03 I see Moayad was busy collecting item views and downloads from CGSpace yesterday: # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Oct/2018" | awk '{print $1} ' | sort | uniq -c | sort -n | tail -n 10 933 40." />
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<meta name="twitter:description" content="2018-10-01 Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now 2018-10-03 I see Moayad was busy collecting item views and downloads from CGSpace yesterday: # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Oct/2018" | awk '{print $1} ' | sort | uniq -c | sort -n | tail -n 10 933 40."/>
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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/2018-10/">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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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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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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<h2 id="2018-10-03">2018-10-03</h2>
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<ul>
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<li>I see Moayad was busy collecting item views and downloads from CGSpace yesterday:</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/Oct/2018" | awk '{print $1}
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' | sort | uniq -c | sort -n | tail -n 10
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933 40.77.167.90
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971 95.108.181.88
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1043 41.204.190.40
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1454 157.55.39.54
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1538 207.46.13.69
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1719 66.249.64.61
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2048 50.116.102.77
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4639 66.249.64.59
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4736 35.237.175.180
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150362 34.218.226.147
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</code></pre>
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<ul>
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<li>Of those, about 20% were HTTP 500 responses (!):</li>
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</ul>
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<pre><code>$ zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Oct/2018" | grep 34.218.226.147 | awk '{print $9}' | sort -n | uniq -c
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118927 200
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31435 500
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</code></pre>
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<ul>
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<li>I added Phil Thornton and Sonal Henson’s ORCID identifiers to the controlled vocabulary for <code>cg.creator.orcid</code> and then re-generated the names using my <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script:</li>
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</ul>
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<pre><code>$ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml | sort | uniq > 2018-10-03-orcids.txt
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$ ./resolve-orcids.py -i 2018-10-03-orcids.txt -o 2018-10-03-names.txt -d
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</code></pre>
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<ul>
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<li>I found a new corner case error that I need to check, given <em>and</em> family names deactivated:</li>
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</ul>
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<pre><code>Looking up the names associated with ORCID iD: 0000-0001-7930-5752
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Given Names Deactivated Family Name Deactivated: 0000-0001-7930-5752
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</code></pre>
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<ul>
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<li>It appears to be Jim Lorenzen… I need to check that later!</li>
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<li>I merged the changes to the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/390">#390</a>)</li>
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<li>Linode sent another alert about CPU usage on CGSpace (linode18) this evening</li>
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<li>It seems that Moayad is making quite a lot of requests today:</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 "03/Oct/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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1594 157.55.39.160
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1627 157.55.39.173
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1774 136.243.6.84
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4228 35.237.175.180
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4497 70.32.83.92
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4856 66.249.64.59
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7120 50.116.102.77
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12518 138.201.49.199
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87646 34.218.226.147
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111729 213.139.53.62
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</code></pre>
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<ul>
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<li>But in super positive news, he says they are using my new <a href="https://github.com/alanorth/dspace-statistics-api">dspace-statistics-api</a> and it’s MUCH faster than using Atmire CUA’s internal “restlet” API</li>
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<li>I don’t recognize the <code>138.201.49.199</code> IP, but it is in Germany (Hetzner) and appears to be paginating over some browse pages and downloading bitstreams:</li>
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</ul>
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<pre><code># grep 138.201.49.199 /var/log/nginx/access.log | grep -o -E 'GET /[a-z]+' | sort | uniq -c
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8324 GET /bitstream
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4193 GET /handle
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</code></pre>
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<ul>
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<li>Suspiciously, it’s only grabbing the CGIAR System Office community (handle prefix 10947):</li>
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</ul>
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<pre><code># grep 138.201.49.199 /var/log/nginx/access.log | grep -o -E 'GET /handle/[0-9]{5}' | sort | uniq -c
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7 GET /handle/10568
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4186 GET /handle/10947
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</code></pre>
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<ul>
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<li>The user agent is suspicious too:</li>
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</ul>
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<pre><code>Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2227.0 Safari/537.36
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</code></pre>
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<ul>
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<li>It’s clearly a bot and it’s not re-using its Tomcat session, so I will add its IP to the nginx bad bot list</li>
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<li>I looked in Solr’s statistics core and these hits were actually all counted as <code>isBot:false</code> (of course)… hmmm</li>
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<li>I tagged all of Sonal and Phil’s items with their ORCID identifiers on CGSpace using my <a href="https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050">add-orcid-identifiers.py</a> script:</li>
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</ul>
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<pre><code>$ ./add-orcid-identifiers-csv.py -i 2018-10-03-add-orcids.csv -db dspace -u dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>Where <code>2018-10-03-add-orcids.csv</code> contained:</li>
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</ul>
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<pre><code>dc.contributor.author,cg.creator.id
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"Henson, Sonal P.",Sonal Henson: 0000-0002-2002-5462
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"Henson, S.",Sonal Henson: 0000-0002-2002-5462
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"Thornton, P.K.",Philip Thornton: 0000-0002-1854-0182
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"Thornton, Philip K",Philip Thornton: 0000-0002-1854-0182
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"Thornton, Phil",Philip Thornton: 0000-0002-1854-0182
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"Thornton, Philip K.",Philip Thornton: 0000-0002-1854-0182
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"Thornton, Phillip",Philip Thornton: 0000-0002-1854-0182
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"Thornton, Phillip K.",Philip Thornton: 0000-0002-1854-0182
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</code></pre>
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<h2 id="2018-10-04">2018-10-04</h2>
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<ul>
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<li>Salem raised an issue that the dspace-statistics-api reports downloads for some items that have no bitstreams (like many limited access items)</li>
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<li>Every item has at least a <code>LICENSE</code> bundle, and some have a <code>THUMBNAIL</code> bundle, but the indexing code is specifically checking for downloads from the <code>ORIGINAL</code> bundle
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<ul>
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<li><a href="https://cgspace.cgiar.org/handle/10568/97460"><sup>10568</sup>⁄<sub>97460</sub></a> (100550): has a thumbnail bitstream</li>
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<li><a href="https://cgspace.cgiar.org/handle/10568/96112"><sup>10568</sup>⁄<sub>96112</sub></a> (96736): has only a LICENSE bitstream</li>
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</ul></li>
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<li>I see there are other bundles we might need to pay attention to: <code>TEXT</code>, <code>@_LOGO-COLLECTION_@</code>, <code>@_LOGO-COMMUNITY_@</code>, etc…</li>
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<li>On a hunch I dropped the statistics table and re-indexed and now those two items above have no downloads</li>
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<li>So it’s fixed, but I’m not sure why!</li>
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<li>Peter wants to know the number of API requests per month, which was about 250,000 in September (exluding statlet requests):</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/{oai,rest}.log* | grep -E 'Sep/2018' | grep -c -v 'statlets'
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251226
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</code></pre>
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<ul>
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<li>I found a logic error in the dspace-statistics-api <code>indexer.py</code> script that was causing item views to be inserted into downloads</li>
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<li>I tagged version 0.4.2 of the tool and redeployed it on CGSpace</li>
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</ul>
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<h2 id="2018-10-05">2018-10-05</h2>
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<ul>
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<li>Meet with Peter, Abenet, and Sisay to discuss CGSpace meeting in Nairobi and Sisay’s work plan</li>
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<li>We agreed that he would do monthly updates of the controlled vocabularies and generate a new one for the top 1,000 AGROVOC terms</li>
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<li>Add a link to <a href="https://cgspace.cgiar.org/explorer/">AReS explorer</a> to the CGSpace homepage introduction text</li>
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</ul>
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<h2 id="2018-10-06">2018-10-06</h2>
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<ul>
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<li>Follow up with AgriKnowledge about including Handle links (<code>dc.identifier.uri</code>) on their item pages</li>
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<li>In July, 2018 they had said their programmers would include the field in the next update of their website software</li>
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<li><a href="https://repository.cimmyt.org/">CIMMYT’s DSpace repository</a> is now running DSpace 5.x!</li>
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<li>It’s running OAI, but not REST, so I need to talk to Richard about that!</li>
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</ul>
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<h2 id="2018-10-08">2018-10-08</h2>
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<ul>
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<li>AgriKnowledge says they’re going to add the <code>dc.identifier.uri</code> to their item view in November when they update their website software</li>
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</ul>
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<h2 id="2018-10-10">2018-10-10</h2>
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<ul>
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<li>Peter noticed that some recently added PDFs don’t have thumbnails</li>
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<li>When I tried to force them to be generated I got an error that I’ve never seen before:</li>
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</ul>
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<pre><code>$ dspace filter-media -v -f -i 10568/97613
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org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: not authorized `/tmp/impdfthumb5039464037201498062.pdf' @ error/constitute.c/ReadImage/412.
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</code></pre>
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<ul>
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<li>I see there was an update to Ubuntu’s ImageMagick on 2018-10-05, so maybe something changed or broke?</li>
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<li>I get the same error when forcing <code>filter-media</code> to run on DSpace Test too, so it’s gotta be an ImageMagic bug</li>
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<li>The ImageMagick version is currently 8:6.8.9.9-7ubuntu5.13, and there is an <a href="https://usn.ubuntu.com/3785-1/">Ubuntu Security Notice from 2018-10-04</a></li>
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<li>Wow, someone on <a href="https://twitter.com/rosscampbell/status/1048268966819319808">Twitter posted about this breaking his web application</a> (and it was retweeted by the ImageMagick acount!)</li>
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<li>I commented out the line that disables PDF thumbnails in <code>/etc/ImageMagick-6/policy.xml</code>:</li>
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</ul>
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<pre><code> <!--<policy domain="coder" rights="none" pattern="PDF" />-->
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</code></pre>
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<ul>
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<li>This works, but I’m not sure what ImageMagick’s long-term plan is if they are going to disable ALL image formats…</li>
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<li>I suppose I need to enable a workaround for this in Ansible?</li>
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<li>Also I note that for a few days the item views on DSpace Test are broken… I think Sisay must have been doing something</li>
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</ul>
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<h2 id="2018-10-11">2018-10-11</h2>
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<ul>
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<li>I emailed DuraSpace to update <a href="https://duraspace.org/registry/entry/4188/?gvid=178">our entry in their DSpace registry</a> (the data was still on DSpace 3, JSPUI, etc)</li>
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<li>Generate a list of the top 1500 values for <code>dc.subject</code> so Sisay can start making a controlled vocabulary for it:</li>
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</ul>
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<pre><code>dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 57 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2018-10-11-top-1500-subject.csv WITH CSV HEADER;
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COPY 1500
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</code></pre>
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<!-- vim: set sw=2 ts=2: -->
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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/2018-10/">October, 2018</a></li>
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<li><a href="/cgspace-notes/2018-09/">September, 2018</a></li>
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<li><a href="/cgspace-notes/2018-08/">August, 2018</a></li>
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<li><a href="/cgspace-notes/2018-07/">July, 2018</a></li>
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<li><a href="/cgspace-notes/2018-06/">June, 2018</a></li>
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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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