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May, 2016 · CGSpace Notes
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<article>
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<header>
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<h1 class="text-primary">May, 2016</h1>
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<div class="post-meta clearfix">
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<div class="post-date pull-left">
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Posted on
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<time datetime="2016-05-01T23:06:00+03:00">
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May 1, 2016
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</time>
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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</div>
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</header>
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<section>
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<h2 id="2016-05-01:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-01</h2>
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<ul>
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<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
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<li>I have blocked access to the API now</li>
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<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
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</ul>
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<pre><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
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3168
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</code></pre>
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<ul>
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<li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li>
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<li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li>
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</ul>
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<pre><code>GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1
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</code></pre>
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<ul>
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<li>For now I’ll block just the Ethiopian IP</li>
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<li>The owner of that application has said that the <code>NaN</code> (not a number) is an error in his code and he’ll fix it</li>
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</ul>
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<h2 id="2016-05-03:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-03</h2>
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<ul>
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<li>Update nginx to 1.10.x branch on CGSpace</li>
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<li>Fix a reference to <code>dc.type.output</code> in Discovery that I had missed when we migrated to <code>dc.type</code> last month (<a href="https://github.com/ilri/DSpace/pull/223">#223</a>)</li>
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</ul>
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<p><img src="../images/2016/05/discovery-types.png" alt="Item type in Discovery results" /></p>
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<h2 id="2016-05-06:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-06</h2>
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<ul>
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<li>DSpace Test is down, <code>catalina.out</code> has lots of messages about heap space from some time yesterday (!)</li>
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<li>It looks like Sisay was doing some batch imports</li>
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<li>Hmm, also disk space is full</li>
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<li>I decided to blow away the solr indexes, since they are 50GB and we don’t really need all the Atmire stuff there right now</li>
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<li>I will re-generate the Discovery indexes after re-deploying</li>
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<li>Testing <code>renew-letsencrypt.sh</code> script for nginx</li>
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</ul>
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<pre><code>#!/usr/bin/env bash
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readonly SERVICE_BIN=/usr/sbin/service
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readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto
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# stop nginx so LE can listen on port 443
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$SERVICE_BIN nginx stop
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$LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 > /var/log/letsencrypt/renew.log 2>&1
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LE_RESULT=$?
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$SERVICE_BIN nginx start
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if [[ "$LE_RESULT" != 0 ]]; then
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echo 'Automated renewal failed:'
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cat /var/log/letsencrypt/renew.log
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exit 1
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fi
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</code></pre>
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<ul>
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<li>Seems to work well</li>
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</ul>
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<h2 id="2016-05-10:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-10</h2>
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<ul>
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<li>Start looking at more metadata migrations</li>
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<li>There are lots of fields in <code>dcterms</code> namespace that look interesting, like:
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<ul>
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<li>dcterms.type</li>
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<li>dcterms.spatial</li>
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</ul></li>
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<li>Not sure what <code>dcterms</code> is…</li>
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<li>Looks like these were <a href="https://wiki.duraspace.org/display/DSDOC5x/Metadata+and+Bitstream+Format+Registries#MetadataandBitstreamFormatRegistries-DublinCoreTermsRegistry(DCTERMS)">added in DSpace 4</a> to allow for future work to make DSpace more flexible</li>
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<li>CGSpace’s <code>dc</code> registry has 96 items, and the default DSpace one has 73.</li>
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</ul>
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<h2 id="2016-05-11:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-11</h2>
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<ul>
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<li><p>Identify and propose the next phase of CGSpace fields to migrate:</p>
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<ul>
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<li>dc.title.jtitle → cg.title.journal</li>
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<li>dc.identifier.status → cg.identifier.status</li>
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<li>dc.river.basin → cg.river.basin</li>
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<li>dc.Species → cg.species</li>
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<li>dc.targetaudience → cg.targetaudience</li>
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<li>dc.fulltextstatus → cg.fulltextstatus</li>
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<li>dc.editon → cg.edition</li>
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<li>dc.isijournal → cg.isijournal</li>
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</ul></li>
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<li><p>Start a test rebase of the <code>5_x-prod</code> branch on top of the <code>dspace-5.5</code> tag</p></li>
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<li><p>There were a handful of conflicts that I didn’t understand</p></li>
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<li><p>After completing the rebase I tried to build with the module versions Atmire had indicated as being 5.5 ready but I got this error:</p></li>
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</ul>
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<pre><code>[ERROR] Failed to execute goal on project additions: Could not resolve dependencies for project org.dspace.modules:additions:jar:5.5: Could not find artifact com.atmire:atmire-metadata-quality-api:jar:5.5-2.10.1-0 in sonatype-releases (https://oss.sonatype.org/content/repositories/releases/) -> [Help 1]
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</code></pre>
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<ul>
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<li>I’ve sent them a question about it</li>
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<li>A user mentioned having problems with uploading a 33 MB PDF</li>
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<li>I told her I would increase the limit temporarily tomorrow morning</li>
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<li>Turns out she was able to decrease the size of the PDF so we didn’t have to do anything</li>
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</ul>
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<h2 id="2016-05-12:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-12</h2>
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<ul>
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<li>Looks like the issue that Abenet was having a few days ago with “Connection Reset” in Firefox might be due to a Firefox 46 issue: <a href="https://bugzilla.mozilla.org/show_bug.cgi?id=1268775">https://bugzilla.mozilla.org/show_bug.cgi?id=1268775</a></li>
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<li>I finally found a copy of the latest CG Core metadata guidelines and it looks like we can add a few more fields to our next migration:
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<ul>
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<li>dc.rplace.region → cg.coverage.region</li>
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<li>dc.cplace.country → cg.coverage.country</li>
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</ul></li>
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<li>Questions for CG people:
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<ul>
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<li>Our <code>dc.place</code> and <code>dc.srplace.subregion</code> could both map to <code>cg.coverage.admin-unit</code>?</li>
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<li>Should we use <code>dc.contributor.crp</code> or <code>cg.contributor.crp</code> for the CRP (ours is <code>dc.crsubject.crpsubject</code>)?</li>
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<li>Our <code>dc.contributor.affiliation</code> and <code>dc.contributor.corporate</code> could both map to <code>dc.contributor</code> and possibly <code>dc.contributor.center</code> depending on if it’s a CG center or not</li>
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<li><code>dc.title.jtitle</code> could either map to <code>dc.publisher</code> or <code>dc.source</code> depending on how you read things</li>
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</ul></li>
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<li>Found ~200 messed up CIAT values in <code>dc.publisher</code>:</li>
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</ul>
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<pre><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "% %";
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</code></pre>
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<h2 id="2016-05-13:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-13</h2>
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<ul>
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<li>More theorizing about CGcore</li>
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<li>Add two new fields:
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<ul>
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<li>dc.srplace.subregion → cg.coverage.admin-unit</li>
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<li>dc.place → cg.place</li>
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</ul></li>
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<li><code>dc.place</code> is our own field, so it’s easy to move</li>
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<li>I’ve removed <code>dc.title.jtitle</code> from the list for now because there’s no use moving it out of DC until we know where it will go (see discussion yesterday)</li>
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</ul>
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<h2 id="2016-05-18:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-18</h2>
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<ul>
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<li>Work on 707 CCAFS records</li>
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<li>They have thumbnails on Flickr and elsewhere</li>
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<li>In OpenRefine I created a new <code>filename</code> column based on the <code>thumbnail</code> column with the following GREL:</li>
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</ul>
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<pre><code>if(cells['thumbnails'].value.contains('hqdefault'), cells['thumbnails'].value.split('/')[-2] + '.jpg', cells['thumbnails'].value.split('/')[-1])
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</code></pre>
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<ul>
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<li>Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL</li>
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<li>So for the <code>hqdefault.jpg</code> ones I just take the UUID (-2) and use it as the filename</li>
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<li>Before importing with SAFBuilder I tested adding “__bundle:THUMBNAIL” to the <code>filename</code> column and it works fine</li>
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</ul>
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<h2 id="2016-05-19:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-19</h2>
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<ul>
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<li>More quality control on <code>filename</code> field of CCAFS records to make processing in shell and SAFBuilder more reliable:</li>
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</ul>
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<pre><code>value.replace('_','').replace('-','')
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</code></pre>
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<ul>
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<li>We need to hold off on moving <code>dc.Species</code> to <code>cg.species</code> because it is only used for plants, and might be better to move it to something like <code>cg.species.plant</code></li>
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<li>And <code>dc.identifier.fund</code> is MOSTLY used for CPWF project identifier but has some other sponsorship things
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<ul>
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<li>We should move PN<em>, SG</em>, CBA, IA, and PHASE* values to <code>cg.identifier.cpwfproject</code></li>
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<li>The rest, like BMGF and USAID etc, might have to go to either <code>dc.description.sponsorship</code> or <code>cg.identifier.fund</code> (not sure yet)</li>
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<li>There are also some mistakes in CPWF’s things, like “PN 47”</li>
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<li>This ought to catch all the CPWF values (there don’t appear to be and SG* values):</li>
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</ul></li>
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</ul>
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<pre><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
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</code></pre>
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<h2 id="2016-05-20:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-20</h2>
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<ul>
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<li>More work on CCAFS Video and Images records</li>
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<li>For SAFBuilder we need to modify filename column to have the thumbnail bundle:
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<br /></li>
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</ul>
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<pre><code>value + "__bundle:THUMBNAIL"
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</code></pre>
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<ul>
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<li>Also, I fixed some weird characters using OpenRefine’s transform with the following GREL:</li>
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</ul>
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<pre><code>value.replace(/\u0081/,'')
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</code></pre>
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<ul>
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<li>Write shell script to resize thumbnails with height larger than 400: <a href="https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256">https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256</a></li>
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<li>Upload 707 CCAFS records to DSpace Test</li>
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<li>A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target <code>_black</code>): <a href="https://github.com/ilri/DSpace/pull/224">#224</a></li>
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<li>Work on configuration changes for Phase 2 metadata migrations</li>
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</ul>
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<h2 id="2016-05-23:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-23</h2>
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<ul>
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<li>Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine</li>
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<li>LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.</li>
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<li>Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don’t match!</li>
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<li>I will have to try later</li>
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</ul>
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<h2 id="2016-05-30:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-30</h2>
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<ul>
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<li>Export CCAFS video and image records from DSpace Test using the migrate option (<code>-m</code>):</li>
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</ul>
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<pre><code>$ mkdir ~/ccafs-images
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$ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m
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</code></pre>
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<ul>
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<li>And then import to CGSpace:</li>
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</ul>
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<pre><code>$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/70974 --source /tmp/ccafs-images --mapfile=/tmp/ccafs-images-may30.map &> /tmp/ccafs-images-may30.log
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</code></pre>
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<ul>
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<li>But now we have double authors for “CGIAR Research Program on Climate Change, Agriculture and Food Security” in the authority</li>
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<li>I’m trying to do a Discovery index before messing with the authority index</li>
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<li>Looks like we are missing the <code>index-authority</code> cron job, so who knows what’s up with our authority index</li>
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<li>Run system updates on DSpace Test, re-deploy code, and reboot the server</li>
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<li>Clean up and import ~200 CTA records to CGSpace via CSV like:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8"
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$ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &> ~/CTA-May30/CTA-42229.log
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</code></pre>
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<ul>
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<li>Discovery indexing took a few hours for some reason, and after that I started the <code>index-authority</code> script</li>
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</ul>
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<pre><code>$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority
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</code></pre>
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<h2 id="2016-05-31:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-31</h2>
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<ul>
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<li>The <code>index-authority</code> script ran over night and was finished in the morning</li>
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<li>Hopefully this was because we haven’t been running it regularly and it will speed up next time</li>
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<li>I am running it again with a timer to see:</li>
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</ul>
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<pre><code>$ time /home/cgspace.cgiar.org/bin/dspace index-authority
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Retrieving all data
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Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
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Cleaning the old index
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Writing new data
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All done !
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real 37m26.538s
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user 2m24.627s
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sys 0m20.540s
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</code></pre>
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<ul>
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<li>Update <code>tomcat7</code> crontab on CGSpace and DSpace Test to have the <code>index-authority</code> script that we were missing</li>
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<li>Add new ILRI subject and CCAFS project tags to <code>input-forms.xml</code> (<a href="https://github.com/ilri/DSpace/pull/226">#226</a>, <a href="https://github.com/ilri/DSpace/pull/225">#225</a>)</li>
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<li>Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.</li>
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</ul>
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</section>
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<footer>
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<section class="author-info row">
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<div class="author-avatar col-md-2">
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</div>
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<div class="author-meta col-md-6">
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<h1 class="author-name text-primary">Alan Orth</h1>
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