<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta property="og:title" content="June, 2018" /> <meta property="og:description" content="2018-06-04 Test the DSpace 5.8 module upgrades from Atmire (#378) 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 I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379) I proofed and tested the ILRI author corrections that Peter sent back to me this week: $ ./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 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 Time to index ~70,000 items on CGSpace: $ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b real 74m42.646s user 8m5.056s sys 2m7.289s " /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-06/" /> <meta property="article:published_time" content="2018-06-04T19:49:54-07:00"/> <meta property="article:modified_time" content="2018-06-10T14:12:07+03:00"/> <meta name="twitter:card" content="summary"/> <meta name="twitter:title" content="June, 2018"/> <meta name="twitter:description" content="2018-06-04 Test the DSpace 5.8 module upgrades from Atmire (#378) 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 I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379) I proofed and tested the ILRI author corrections that Peter sent back to me this week: $ ./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 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 Time to index ~70,000 items on CGSpace: $ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b real 74m42.646s user 8m5.056s sys 2m7.289s "/> <meta name="generator" content="Hugo 0.40.3" /> <script type="application/ld+json"> { "@context": "http://schema.org", "@type": "BlogPosting", "headline": "June, 2018", "url": "https://alanorth.github.io/cgspace-notes/2018-06/", "wordCount": "750", "datePublished": "2018-06-04T19:49:54-07:00", "dateModified": "2018-06-10T14:12:07+03:00", "author": { "@type": "Person", "name": "Alan Orth" }, "keywords": "Notes" } </script> <link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-06/"> <title>June, 2018 | CGSpace Notes</title> <!-- combined, minified CSS --> <link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-ZwlQQbzhEPf3PrXZ3h/XKT/4UHafQ/TYI72AL+7WOJ8D6JmpGC8JMMse6xX7cyeI" crossorigin="anonymous"> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1> <p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-06/">June, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-06-04T19:49:54-07:00">Mon Jun 04, 2018</time> by Alan Orth in <i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a> </p> </header> <h2 id="2018-06-04">2018-06-04</h2> <ul> <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>) <ul> <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> </ul></li> <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> <li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li> </ul> <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 </code></pre> <ul> <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> <li>Time to index ~70,000 items on CGSpace:</li> </ul> <pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b real 74m42.646s user 8m5.056s sys 2m7.289s </code></pre> <p></p> <h2 id="2018-06-06">2018-06-06</h2> <ul> <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> <li>Now Maven and Ant run properly, but I’m getting SQL migration errors in <code>dspace.log</code> after starting Tomcat</li> <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> </ul> <h2 id="2018-06-07">2018-06-07</h2> <ul> <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> <ul> <li>Mispelled authorship type: CGAIR single center should be: CGIAR single centre</li> <li>I see some encoding errors in author affiliations, for example:</li> <li>Universidade de SÆo Paulo</li> <li>Institut National des Recherches Agricoles du B nin</li> <li>Centre de Coop ration Internationale en Recherche Agronomique pour le D veloppement</li> <li>Institut des Recherches Agricoles du B nin</li> <li>Institut des Savannes, C te d’ Ivoire</li> <li>Institut f r Pflanzenpathologie und Pflanzenschutz der Universit t, Germany</li> <li>Projet de Gestion des Ressources Naturelles, B nin</li> <li>Universit t Hannover</li> <li>Universit F lix Houphouet-Boigny</li> </ul></li> <li>I uploaded fixes for all those now, but I will continue with the rest of the data later</li> <li>Regarding the SQL migration errors, Atmire told me I need to run some migrations manually in PostgreSQL:</li> </ul> <pre><code>delete from schema_version where version = '5.6.2015.12.03.2'; update schema_version set version = '5.6.2015.12.03.2' where version = '5.5.2015.12.03.2'; update schema_version set version = '5.8.2015.12.03.3' where version = '5.5.2015.12.03.3'; </code></pre> <ul> <li>And then I need to ignore the ignored ones:</li> </ul> <pre><code>$ ~/dspace/bin/dspace database migrate ignored </code></pre> <ul> <li>Now DSpace starts up properly!</li> <li>Gabriela from CIP got back to me about the author names we were correcting on CGSpace</li> <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> </ul> <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 </code></pre> <ul> <li>I will apply them on CGSpace tomorrow I think…</li> </ul> <h2 id="2018-06-09">2018-06-09</h2> <ul> <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> <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> <li>I applied the CIP author corrections on CGSpace and DSpace Test and re-ran the Discovery indexing</li> </ul> <h2 id="2018-06-10">2018-06-10</h2> <ul> <li>I spent some time removing the Atmire Metadata Quality Module (MQM) from the proposed DSpace 5.8 changes</li> <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> </ul> <pre><code> INFO [org.dspace.servicemanager.DSpaceServiceManager] Shutdown DSpace core service manager 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]; </code></pre> <ul> <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> <li>I will have to ask Atmire</li> <li>I continued to look at Sisay’s IITA records from last week <ul> <li>I normalized all DOIs to use HTTPS and “doi.org” instead of “dx.doi.org”</li> <li>I cleaned up white space in <code>cg.subject.iita</code> and <code>dc.subject</code></li> <li>Even a bunch of IITA and AGROVOC subjects are missing accents, ie “FERTILIT DU SOL”</li> <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> <li>A few dozen items have abstracts with character encoding errors, ie:</li> <li>33.7øC</li> <li>MgSO4ú7H2O</li> <li>ha??1&/sup;</li> <li>En gen6ral</li> <li>dÕpassÕ</li> <li>Also the abstracts have missing accents, ie “recherche sur le d veloppement”</li> </ul></li> <li>I will have to tell IITA people to redo these entirely I think…</li> </ul> </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 --> <footer class="blog-footer"> <p> Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>. </p> <p> <a href="#">Back to top</a> </p> </footer> </body> </html>