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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="2018-06-12T10:42:43+03:00"/>
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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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||
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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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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-06/">
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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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<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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<li>I continued to look at Sisay’s IITA records from last week
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<ul>
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<li>I normalized all DOIs to use HTTPS and “doi.org” instead of “dx.doi.org”</li>
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<li>I cleaned up white space in <code>cg.subject.iita</code> and <code>dc.subject</code></li>
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<li>Even a bunch of IITA and AGROVOC subjects are missing accents, ie “FERTILIT DU SOL”</li>
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<li>More organization names in <code>dc.description.sponsorship</code> are incorrect (ie, missing accents) or inconsistent (ie, CGIAR centers should be spelled in English or multiple spellings of the same one, like “Rockefeller Foundation” and “Rockefeller foundation”)</li>
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<li>A few dozen items have abstracts with character encoding errors, ie:</li>
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<li>33.7øC</li>
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<li>MgSO4ú7H2O</li>
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<li>ha??1&/sup;</li>
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<li>En gen6ral</li>
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<li>dÕpassÕ</li>
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<li>Also the abstracts have missing accents, ie “recherche sur le d veloppement”</li>
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</ul></li>
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<li>I will have to tell IITA people to redo these entirely I think…</li>
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</ul>
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<h2 id="2018-06-11">2018-06-11</h2>
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<ul>
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<li>Sisay sent a new version of the last IITA records that he created from the original CSV from IITA</li>
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<li>The 200 records are in the <a href="https://dspacetest.cgiar.org/handle/10568/95870">IITA_Junel_11 (<sup>10568</sup>⁄<sub>95870</sub>)</a> collection</li>
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<li>Many errors:
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<ul>
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<li>Authorship types: “CGIAR ans advanced research institute”, “CGAIR and advanced research institute”, “CGIAR and advanced research institutes”, “CGAIR single center”</li>
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<li>Lots of inconsistencies and mispellings in author affiliations:</li>
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<li>“Institut des Recherches Agricoles du Bénin” and “Institut National des Recherche Agricoles du Benin” and “National Agricultural Research Institute, Benin”</li>
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<li>International Insitute of Tropical Agriculture</li>
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<li>Centro Internacional de Agricultura Tropical</li>
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<li>“Rivers State University of Science and Technology” and “Rivers State University”</li>
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<li>“Institut de la Recherche Agronomique, Cameroon” and “Institut de Recherche Agronomique, Cameroon”</li>
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<li>Inconsistency in countries: “COTE D’IVOIRE” and “COTE D’IVOIRE”</li>
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<li>A few DOIs with spaces or invalid characters</li>
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<li>Inconsistency in IITA subjects, for example “PRODUCTION VEGETALE” and “PRODUCTION VÉGÉTALE” and several others</li>
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<li>I ran <code>value.unescape('javascript')</code> on the abstract and citation fields because it looks like this data came from a SQL database and some stuff was escaped</li>
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</ul></li>
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<li>It turns out that Abenet actually did a lot of small corrections on this data so when Sisay uses Bosede’s original file it doesn’t have all those corrections</li>
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<li>So I told Sisay to re-create the collection using Abenet’s XLS from last week (<code>Mercy1805_AY.xls</code>)</li>
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<li>I was curious to see if I could create a GREL for use with a custom text facet in Open Refine to find cells with two or more consecutive spaces</li>
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<li>I always use the built-in trim and collapse transformations anyways, but this seems to work to find the offending cells: <code>isNotNull(value.match(/.*?\s{2,}.*?/))</code></li>
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<li>I wonder if I should start checking for “smart” quotes like ’ (hex 2019)</li>
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</ul>
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<h2 id="2018-06-12">2018-06-12</h2>
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<ul>
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<li>Udana from IWMI asked about the OAI base URL for their community on CGSpace</li>
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<li>I think it should be this: <a href="https://cgspace.cgiar.org/oai/request?verb=ListRecords&metadataPrefix=oai_dc&set=com_10568_16814">https://cgspace.cgiar.org/oai/request?verb=ListRecords&metadataPrefix=oai_dc&set=com_10568_16814</a></li>
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<li>The style sheet obfuscates the data, but if you look at the source it is all there, including information about pagination of results</li>
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<li>Regarding Udana’s Book Chapters and Reports on DSpace Test last week, Abenet told him to fix some character encoding and CRP issues, then I told him I’d check them after that</li>
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<li>The latest batch of IITA’s 200 records (based on Abenet’s version <code>Mercy1805_AY.xls</code>) are now in the <a href="https://dspacetest.cgiar.org/handle/10568/96071">IITA_Jan_9_II_Ab</a> collection</li>
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<li>So here are some corrections:
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<ul>
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<li>use of Unicode smart quote (hex 2019) in countries and affiliations, for example “COTE D’IVOIRE” and “Institut d’Economic Rurale, Mali”</li>
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<li>inconsistencies in <code>cg.contributor.affiliation</code>:</li>
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<li>“Centro Internacional de Agricultura Tropical” and “Centro International de Agricultura Tropical” should use the English name of CIAT (International Center for Tropical Agriculture)</li>
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<li>“Institut International d’Agriculture Tropicale” should use the English name of IITA (International Institute of Tropical Agriculture)</li>
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<li>“East and Southern Africa Regional Center” and “Eastern and Southern Africa Regional Centre”</li>
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<li>“Institut de la Recherche Agronomique, Cameroon” and “Institut de Recherche Agronomique, Cameroon”</li>
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<li>“Institut des Recherches Agricoles du Bénin” and “Institut National des Recherche Agricoles du Benin” and “National Agricultural Research Institute, Benin”</li>
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<li>“Institute of Agronomic Research, Cameroon” and “Institute of Agronomy Research, Cameroon”</li>
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<li>“Rivers State University” and “Rivers State University of Science and Technology”</li>
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<li>“Universität Hannover” and “University of Hannover”</li>
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<li>inconsistencies in <code>cg.subject.iita</code>:</li>
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<li>“AMELIORATION DES PLANTES” and “AMÉLIORATION DES PLANTES”</li>
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<li>“PRODUCTION VEGETALE” and “PRODUCTION VÉGÉTALE”</li>
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<li>“CONTRÔLE DE MALADIES” and “CONTROLE DES MALADIES”</li>
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<li>“HANDLING, TRANSPORT, STORAGE AND PROTECTION OF AGRICULTURAL PRODUCT” and “HANDLING, TRANSPORT, STORAGE AND PROTECTION OF AGRICULTURAL PRODUCTS”</li>
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<li>“RAVAGEURS DE PLANTES” and “RAVAGEURS DES PLANTES”</li>
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<li>“SANTE DES PLANTES” and “SANTÉ DES PLANTES”</li>
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<li>“SOCIOECONOMIE” and “SOCIOECONOMY”</li>
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<li>inconsistencies in <code>dc.description.sponsorship</code>:</li>
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<li>“Belgian Corporation” and “Belgium Corporation”</li>
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<li>inconsistencies in <code>dc.subject</code>:</li>
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<li>“AFRICAN CASSAVA MOSAIC” and “AFRICAN CASSAVA MOSAIC DISEASE”</li>
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<li>“ASPERGILLU FLAVUS” and “ASPERGILLUS FLAVUS”</li>
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<li>“BIOTECHNOLOGIES” and “BIOTECHNOLOGY”</li>
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<li>“CASSAVA MOSAIC DISEASE” and “CASSAVA MOSAIC DISEASES” and “CASSAVA MOSAIC VIRUS”</li>
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<li>“CASSAVA PROCESSING” and “CASSAVA PROCESSING TECHNOLOGY”</li>
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<li>“CROPPING SYSTEM” and “CROPPING SYSTEMS”</li>
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<li>“DRY SEASON” and “DRY-SEASON”</li>
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<li>“FERTILIZER” and “FERTILIZERS”</li>
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<li>“LEGUME” and “LEGUMES”</li>
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<li>“LEGUMINOSAE” and “LEGUMINOUS”</li>
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<li>“LEGUMINOUS COVER CROP” and “LEGUMINOUS COVER CROPS”</li>
|
||
<li>“MATÉRIEL DE PLANTATION” and “MATÉRIELS DE PLANTATION”</li>
|
||
<li>I noticed that some records do have encoding errors in the <code>dc.description.abstract</code> field, but only four of them so probably not from Abenet’s handling of the XLS file</li>
|
||
<li>Based on manually eyeballing the text I used a custom text facet with this GREL to identify the records:</li>
|
||
</ul></li>
|
||
</ul>
|
||
|
||
<pre><code>or(
|
||
value.contains('€'),
|
||
value.contains('6g'),
|
||
value.contains('6m'),
|
||
value.contains('6d'),
|
||
value.contains('6e')
|
||
)
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>So IITA should double check the abstracts for these:
|
||
|
||
<ul>
|
||
<li><a href="https://dspacetest.cgiar.org/10568/96184">https://dspacetest.cgiar.org/10568/96184</a></li>
|
||
<li><a href="https://dspacetest.cgiar.org/10568/96141">https://dspacetest.cgiar.org/10568/96141</a></li>
|
||
<li><a href="https://dspacetest.cgiar.org/10568/96118">https://dspacetest.cgiar.org/10568/96118</a></li>
|
||
<li><a href="https://dspacetest.cgiar.org/10568/96113">https://dspacetest.cgiar.org/10568/96113</a></li>
|
||
</ul></li>
|
||
</ul>
|
||
|
||
<h2 id="2018-06-13">2018-06-13</h2>
|
||
|
||
<ul>
|
||
<li>Elizabeth from CIAT contacted me to ask if I could add ORCID identifiers to all of Robin Buruchara’s items</li>
|
||
<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>
|
||
</ul>
|
||
|
||
<pre><code>$ ./add-orcid-identifiers-csv.py -i 2018-06-13-Robin-Buruchara.csv -db dspace -u dspace -p 'fuuu'
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>The contents of <code>2018-06-13-Robin-Buruchara.csv</code> were:</li>
|
||
</ul>
|
||
|
||
<pre><code>dc.contributor.author,cg.creator.id
|
||
"Buruchara, Robin",Robin Buruchara: 0000-0003-0934-1218
|
||
"Buruchara, Robin A.",Robin Buruchara: 0000-0003-0934-1218
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>On a hunch I checked to see if CGSpace’s bitstream cleanup was working properly and of course it’s broken:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ dspace cleanup -v
|
||
...
|
||
Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
|
||
Detail: Key (bitstream_id)=(152402) is still referenced from table "bundle".
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>As always, the solution is to delete that ID manually in PostgreSQL:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (152402);'
|
||
UPDATE 1
|
||
</code></pre>
|
||
|
||
<h1 id="vim-set-sw-2-ts-2">vim: set sw=2 ts=2:</h1>
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
</div> <!-- /.blog-main -->
|
||
|
||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2018-06/">June, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-05/">May, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-04/">April, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
</aside>
|
||
|
||
|
||
</div> <!-- /.row -->
|
||
</div> <!-- /.container -->
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||
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||
|
||
|
||
<footer class="blog-footer">
|
||
<p>
|
||
|
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
||
|
||
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|
||
<p>
|
||
<a href="#">Back to top</a>
|
||
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|
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