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<meta property="og:title" content="April, 2018" />
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<meta property="og:description" content="2018-04-01
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I tried to test something on DSpace Test but noticed that it’s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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<meta property="article:published_time" content="2018-04-01T16:13:54+02:00"/>
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<meta property="article:modified_time" content="2018-04-04T15:57:34+03:00"/>
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="April, 2018"/>
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<meta name="twitter:description" content="2018-04-01
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I tried to test something on DSpace Test but noticed that it’s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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"/>
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<meta name="generator" content="Hugo 0.38" />
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-04/">
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<title>April, 2018 | CGSpace Notes</title>
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<header class="blog-header">
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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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<header>
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<h2 class="blog-post-title"><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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<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="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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<p></p>
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<pre><code>Mar 31, 2018 10:26:42 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
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SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
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java.lang.OutOfMemoryError: Java heap space
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Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>So this is getting super annoying</li>
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<li>I ran all system updates on DSpace Test and rebooted it</li>
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<li>For some reason Listings and Reports is not giving any results for any queries now…</li>
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<li>I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module</li>
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<li>Help Lili Szilagyi with a question about statistics on some CCAFS items</li>
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</ul>
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<h2 id="2018-04-04">2018-04-04</h2>
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<ul>
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<li>Peter noticed that there were still some old CRP names on CGSpace, because I hadn’t forced the Discovery index to be updated after I fixed the others last week</li>
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<li>For completeness I re-ran the CRP corrections on CGSpace:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
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Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
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</code></pre>
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<ul>
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<li>Then started a full Discovery index:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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real 76m13.841s
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user 8m22.960s
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sys 2m2.498s
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</code></pre>
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<ul>
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<li>Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme’s items</li>
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<li>I used my <a href="https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py">add-orcid-identifiers-csv.py</a> script:</li>
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</ul>
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<pre><code>$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>The CSV format of <code>jtohme-2018-04-04.csv</code> was:</li>
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</ul>
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<pre><code class="language-csv">dc.contributor.author,cg.creator.id
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"Tohme, Joseph M.",Joe Tohme: 0000-0003-2765-7101
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</code></pre>
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<ul>
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<li>There was a quoting error in my CRP CSV and the replacements for <code>Forests, Trees and Agroforestry</code> got messed up</li>
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<li>So I fixed them and had to re-index again!</li>
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<li>I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:</li>
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</ul>
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<pre><code>$ git checkout -b 5_x-dspace-5.8 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.8
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</code></pre>
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<ul>
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<li>I was prepared to skip some commits that I had cherry picked from the upstream <code>dspace-5_x</code> branch when we did the DSpace 5.5 upgrade (see notes on 2016-10-19 and 2017-12-17):
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<ul>
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<li>[DS-3246] Improve cleanup in recyclable components (upstream commit on dspace-5_x: 9f0f5940e7921765c6a22e85337331656b18a403)</li>
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<li>[DS-3250] applying patch provided by Atmire (upstream commit on dspace-5_x: c6fda557f731dbc200d7d58b8b61563f86fe6d06)</li>
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<li>bump up to latest minor pdfbox version (upstream commit on dspace-5_x: b5330b78153b2052ed3dc2fd65917ccdbfcc0439)</li>
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<li>DS-3583 Usage of correct Collection Array (#1731) (upstream commit on dspace-5_x: c8f62e6f496fa86846bfa6bcf2d16811087d9761)</li>
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</ul></li>
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<li>… but somehow git knew, and didn’t include them in my interactive rebase!</li>
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<li>I need to send this branch to Atmire and also arrange payment (see <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">ticket #560</a> in their tracker)</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 ml-auto 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/2018-04/">April, 2018</a></li>
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<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
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<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
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<li><a href="/cgspace-notes/2017-12/">December, 2017</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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