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2018-06-05 06:31:29 +02:00
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Test the DSpace 5.8 module upgrades from Atmire (#378)
There seems to be a problem with the CUA and L&amp;R versions in pom.xml because they are using SNAPSHOT and it doesn&rsquo;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 &#39;fuuu&#39; -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
Update notes for 2018-06-05
2018-06-06 08:05:37 +02:00
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
Add notes for 2018-06-04
2018-06-05 06:31:29 +02:00
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2018-06-09 10:48:41 +02:00
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Test the DSpace 5.8 module upgrades from Atmire (#378)
There seems to be a problem with the CUA and L&amp;R versions in pom.xml because they are using SNAPSHOT and it doesn&rsquo;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 &#39;fuuu&#39; -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
Update notes for 2018-06-05
2018-06-06 08:05:37 +02:00
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
Add notes for 2018-06-04
2018-06-05 06:31:29 +02:00
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<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>
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<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>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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<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&amp;R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn&rsquo;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>
Update notes for 2018-06-05
2018-06-06 08:05:37 +02:00
<li>Time to index ~70,000 items on CGSpace:</li>
Add notes for 2018-06-04
2018-06-05 06:31:29 +02:00
</ul>
Update notes for 2018-06-05
2018-06-06 08:05:37 +02:00
<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>
Add notes for 2018-06-04
2018-06-05 06:31:29 +02:00
<p></p>
Update notes for 2018-06-06
2018-06-06 19:39:48 +02:00
<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&rsquo;m getting SQL migration errors in <code>dspace.log</code> after starting Tomcat</li>
<li>I&rsquo;ve updated my ticket on Atmire&rsquo;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>
Add notes for 2018-06-07
2018-06-07 18:17:51 +02:00
<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>&frasl;<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&rsquo; 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>
Update notes for 2018-06-07
2018-06-08 08:39:29 +02:00
<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>
Update notes for 2018-06-08
2018-06-08 11:04:27 +02:00
<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&hellip;</li>
Add notes for 2018-06-07
2018-06-07 18:17:51 +02:00
</ul>
Add notes for 2018-06-09
2018-06-09 10:48:41 +02:00
<h2 id="2018-06-09">2018-06-09</h2>
<ul>
<li>It&rsquo;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>
Add notes for 2018-06-04
2018-06-05 06:31:29 +02:00
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<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>
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<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>
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