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<meta property="og:title" content="October, 2016">
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<meta property="article:published_time" content="2016-10-03T15:53:00+03:00">
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<title>October, 2016 | CGSpace Notes</title>
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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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</header>
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<div class="container">
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<div class="row">
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-10/">October, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00+03:00">Mon Oct 03, 2016</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2016-10-03">2016-10-03</h2>
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<ul>
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<li>Testing adding <a href="https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
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<li>Need to test the following scenarios to see how author order is affected:
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<ul>
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<li>ORCIDs only</li>
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<li>ORCIDs plus normal authors</li>
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</ul></li>
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<li>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
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</ul>
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<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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</code></pre>
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<ul>
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<li>Hmm, with the <code>dc.contributor.author</code> column removed, DSpace doesn’t detect any changes</li>
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<li>With a blank <code>dc.contributor.author</code> column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors</li>
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<li>I added the <a href="https://github.com/ilri/DSpace/issues/234">disclaimer text</a> to the About page, then added a footer link to the disclaimer’s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: <a href="https://github.com/twbs/bootstrap/issues/1768">https://github.com/twbs/bootstrap/issues/1768</a></li>
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</ul>
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<p><img src="2016/10/bootstrap-issue.png" alt="Bootstrap issue with in-page anchors" /></p>
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<ul>
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<li>Looks like we’ll just have to add the text to the About page (without a link) or add a separate page</li>
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</ul>
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<h2 id="2016-10-04">2016-10-04</h2>
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<ul>
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<li>Start testing cleanups of authors that Peter sent last week</li>
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<li>Out of 40,000+ rows, Peter had indicated corrections for ~3,200 of them—too many to look through carefully, so I did some basic quality checking:
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<ul>
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<li>Trim leading/trailing whitespace</li>
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<li>Find invalid characters</li>
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<li>Cluster values to merge obvious authors</li>
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</ul></li>
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<li>That left us with 3,180 valid corrections and 3 deletions:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i authors-fix-3180.csv -f dc.contributor.author -t correct -m 3 -d dspacetest -u dspacetest -p fuuu
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$ ./delete-metadata-values.py -i authors-delete-3.csv -f dc.contributor.author -m 3 -d dspacetest -u dspacetest -p fuuu
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</code></pre>
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<ul>
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<li>Remove old about page (<a href="https://github.com/ilri/DSpace/pull/284">#284</a>)</li>
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<li>CGSpace crashed a few times today</li>
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<li>Generate list of unique authors in CCAFS collections:</li>
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</ul>
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<pre><code>dspacetest=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/32729', '10568/5472', '10568/5473', '10568/10288', '10568/70974', '10568/3547', '10568/3549', '10568/3531','10568/16890','10568/5470','10568/3546', '10568/36024', '10568/66581', '10568/21789', '10568/5469', '10568/5468', '10568/3548', '10568/71053', '10568/25167'))) group by text_value order by count desc) to /tmp/ccafs-authors.csv with csv;
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</code></pre>
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<h2 id="2016-10-05">2016-10-05</h2>
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<ul>
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<li>Work on more infrastructure cleanups for Ansible DSpace role</li>
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<li>Clean up Let’s Encrypt plumbing and submit pull request for rmg-ansible-public (<a href="https://github.com/ilri/rmg-ansible-public/pull/60">#60</a>)</li>
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</ul>
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<h2 id="2016-10-06">2016-10-06</h2>
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<ul>
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<li>Nice! DSpace Test (linode02) is now having <code>java.lang.OutOfMemoryError: Java heap space</code> errors…</li>
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<li>Heap space is 2048m, and we have 5GB of RAM being used for OS cache (Solr!) so let’s just bump the memory to 3072m</li>
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<li>Magdalena from CCAFS asked why the colors in the thumbnails for these <a href="https://cgspace.cgiar.org/handle/10568/71249">two</a> <a href="https://cgspace.cgiar.org/handle/10568/71259">items</a> look different, even though they are the same in the PDF itself</li>
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</ul>
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<p><img src="2016/10/cmyk-vs-srgb.jpg" alt="CMYK vs sRGB colors" /></p>
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<ul>
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<li>Turns out the first PDF was exported from InDesign using CMYK and the second one was using sRGB</li>
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<li>Run all system updates on DSpace Test and reboot it</li>
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</ul>
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<h2 id="2016-10-08">2016-10-08</h2>
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<ul>
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<li>Re-deploy CGSpace with latest changes from late September and early October</li>
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<li>Run fixes for ILRI subjects and delete blank metadata values:</li>
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</ul>
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<pre><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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DELETE 11
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</code></pre>
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<ul>
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<li>Run all system updates and reboot CGSpace</li>
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<li>Delete ten gigs of old 2015 Tomcat logs that never got rotated (WTF?):</li>
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</ul>
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<pre><code>root@linode01:~# ls -lh /var/log/tomcat7/localhost_access_log.2015* | wc -l
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47
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</code></pre>
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<ul>
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<li>Delete 2GB <code>cron-filter-media.log</code> file, as it is just a log from a cron job and it doesn’t get rotated like normal log files (almost a year now maybe)</li>
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</ul>
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 offset-sm-1 blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
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<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
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<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
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<li><a href="/cgspace-notes/2016-07/">July, 2016</a></li>
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<li><a href="/cgspace-notes/2016-06/">June, 2016</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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