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<meta property="og:title" content="June, 2018" />
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<meta property="og:description" content="2018-06-04
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Test the DSpace 5.8 module upgrades from Atmire (#378)
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There seems to be a problem with the CUA and L&R versions in pom.xml because they are using SNAPSHOT and it doesn’t build
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I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379)
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I proofed and tested the ILRI author corrections that Peter sent back to me this week:
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$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
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I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in March, 2018
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Time to index ~70,000 items on CGSpace:
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
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real 74m42.646s
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user 8m5.056s
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sys 2m7.289s
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-06/" />
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<meta property="article:published_time" content="2018-06-04T19:49:54-07:00"/>
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<meta property="article:modified_time" content="2018-06-09T11:48:41+03:00"/>
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="June, 2018"/>
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<meta name="twitter:description" content="2018-06-04
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Test the DSpace 5.8 module upgrades from Atmire (#378)
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There seems to be a problem with the CUA and L&R versions in pom.xml because they are using SNAPSHOT and it doesn’t build
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I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379)
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I proofed and tested the ILRI author corrections that Peter sent back to me this week:
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$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
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I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in March, 2018
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Time to index ~70,000 items on CGSpace:
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
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real 74m42.646s
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user 8m5.056s
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sys 2m7.289s
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"/>
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<meta name="generator" content="Hugo 0.40.3" />
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<title>June, 2018 | 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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<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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<article class="blog-post">
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-06/">June, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-06-04T19:49:54-07:00">Mon Jun 04, 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="2018-06-04">2018-06-04</h2>
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<ul>
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<li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>)
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<ul>
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<li>There seems to be a problem with the CUA and L&R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn’t build</li>
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</ul></li>
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<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
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<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
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</code></pre>
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<ul>
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<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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<li>Time to index ~70,000 items on CGSpace:</li>
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</ul>
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<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
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real 74m42.646s
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user 8m5.056s
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sys 2m7.289s
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</code></pre>
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<p></p>
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<h2 id="2018-06-06">2018-06-06</h2>
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<ul>
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<li>It turns out that I needed to add a server block for <code>atmire.com-snapshots</code> to my Maven settings, so now the Atmire code builds</li>
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<li>Now Maven and Ant run properly, but I’m getting SQL migration errors in <code>dspace.log</code> after starting Tomcat</li>
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<li>I’ve updated my ticket on Atmire’s bug tracker: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560</a></li>
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</ul>
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<h2 id="2018-06-07">2018-06-07</h2>
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<ul>
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<li>Proofing 200 IITA records on DSpace Test for Sisay: <a href="https://dspacetest.cgiar.org/handle/10568/95391">IITA_Junel_06 (<sup>10568</sup>⁄<sub>95391</sub>)</a>
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<ul>
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<li>Mispelled authorship type: CGAIR single center should be: CGIAR single centre</li>
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<li>I see some encoding errors in author affiliations, for example:</li>
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<li>Universidade de SÆo Paulo</li>
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<li>Institut National des Recherches Agricoles du B nin</li>
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<li>Centre de Coop ration Internationale en Recherche Agronomique pour le D veloppement</li>
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<li>Institut des Recherches Agricoles du B nin</li>
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<li>Institut des Savannes, C te d’ Ivoire</li>
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<li>Institut f r Pflanzenpathologie und Pflanzenschutz der Universit t, Germany</li>
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<li>Projet de Gestion des Ressources Naturelles, B nin</li>
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<li>Universit t Hannover</li>
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<li>Universit F lix Houphouet-Boigny</li>
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</ul></li>
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<li>I uploaded fixes for all those now, but I will continue with the rest of the data later</li>
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<li>Regarding the SQL migration errors, Atmire told me I need to run some migrations manually in PostgreSQL:</li>
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</ul>
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<pre><code>delete from schema_version where version = '5.6.2015.12.03.2';
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update schema_version set version = '5.6.2015.12.03.2' where version = '5.5.2015.12.03.2';
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update schema_version set version = '5.8.2015.12.03.3' where version = '5.5.2015.12.03.3';
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</code></pre>
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<ul>
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<li>And then I need to ignore the ignored ones:</li>
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</ul>
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<pre><code>$ ~/dspace/bin/dspace database migrate ignored
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</code></pre>
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<ul>
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<li>Now DSpace starts up properly!</li>
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<li>Gabriela from CIP got back to me about the author names we were correcting on CGSpace</li>
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<li>I did a quick sanity check on them and then did a test import with my <a href="https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897"><code>fix-metadata-value.py</code></a> script:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/2018-06-08-CIP-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3
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</code></pre>
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<ul>
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<li>I will apply them on CGSpace tomorrow I think…</li>
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</ul>
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<h2 id="2018-06-09">2018-06-09</h2>
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<ul>
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<li>It’s pretty annoying, but the JVM monitoring for Munin was never set up when I migrated DSpace Test to its new server a few months ago</li>
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<li>I ran the tomcat and munin-node tags in Ansible again and now the stuff is all wired up and recording stats properly</li>
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<li>I applied the CIP author corrections on CGSpace and DSpace Test and re-ran the Discovery indexing</li>
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</ul>
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<h2 id="2018-06-10">2018-06-10</h2>
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<ul>
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<li>I spent some time removing the Atmire Metadata Quality Module (MQM) from the proposed DSpace 5.8 changes</li>
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<li>After removing all code mentioning MQM, mqm, metadata-quality, batchedit, duplicatechecker, etc, I think I got most of it removed, but there is a Spring error during Tomcat startup:</li>
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</ul>
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<pre><code> INFO [org.dspace.servicemanager.DSpaceServiceManager] Shutdown DSpace core service manager
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Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'org.dspace.servicemanager.spring.DSpaceBeanPostProcessor#0' defined in class path resource [spring/spring-dspace-applicationContext.xml]: Unsatisfied dependency expressed through constructor argument with index 0 of type [org.dspace.servicemanager.config.DSpaceConfigurationService]: : Cannot find class [com.atmire.dspace.discovery.ItemCollectionPlugin] for bean with name 'itemCollectionPlugin' defined in file [/home/aorth/dspace/config/spring/api/discovery.xml];
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</code></pre>
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<ul>
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<li>I can fix this by commenting out the <code>ItemCollectionPlugin</code> line of <code>discovery.xml</code>, but from looking at the git log I’m not actually sure if that is related to MQM or not</li>
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<li>I will have to ask Atmire</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/2018-06/">June, 2018</a></li>
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<li><a href="/cgspace-notes/2018-05/">May, 2018</a></li>
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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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</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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