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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
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
2018-06-05 06:31:29 +02:00
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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
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
2018-06-05 06:31:29 +02:00
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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>
<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>
</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&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>
2018-06-06 08:05:37 +02:00
<li>Time to index ~70,000 items on CGSpace:</li>
2018-06-05 06:31:29 +02:00
</ul>
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>
2018-06-05 06:31:29 +02:00
<p></p>
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>
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>
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>
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>
2018-06-07 18:17:51 +02:00
</ul>
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>
2018-06-10 13:12:07 +02:00
<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&rsquo;m not actually sure if that is related to MQM or not</li>
<li>I will have to ask Atmire</li>
2018-06-10 18:32:12 +02:00
<li>I continued to look at Sisay&rsquo;s IITA records from last week
<ul>
<li>I normalized all DOIs to use HTTPS and &ldquo;doi.org&rdquo; instead of &ldquo;dx.doi.org&rdquo;</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 &ldquo;FERTILIT DU SOL&rdquo;</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 &ldquo;Rockefeller Foundation&rdquo; and &ldquo;Rockefeller foundation&rdquo;)</li>
<li>A few dozen items have abstracts with character encoding errors, ie:</li>
<li>33.7øC</li>
<li>MgSO4ú7H2O</li>
<li>ha??1&amp;/sup;</li>
<li>En gen6ral</li>
<li>dÕpassÕ</li>
<li>Also the abstracts have missing accents, ie &ldquo;recherche sur le d veloppement&rdquo;</li>
</ul></li>
<li>I will have to tell IITA people to redo these entirely I think&hellip;</li>
2018-06-10 13:12:07 +02:00
</ul>
2018-06-11 14:21:14 +02:00
<h2 id="2018-06-11">2018-06-11</h2>
<ul>
<li>Sisay sent a new version of the last IITA records that he created from the original CSV from IITA</li>
<li>The 200 records are in the <a href="https://dspacetest.cgiar.org/handle/10568/95870">IITA_Junel_11 (<sup>10568</sup>&frasl;<sub>95870</sub>)</a> collection</li>
<li>Many errors:
<ul>
<li>Authorship types: &ldquo;CGIAR ans advanced research institute&rdquo;, &ldquo;CGAIR and advanced research institute&rdquo;, &ldquo;CGIAR and advanced research institutes&rdquo;, &ldquo;CGAIR single center&rdquo;</li>
<li>Lots of inconsistencies and mispellings in author affiliations:</li>
<li>&ldquo;Institut des Recherches Agricoles du Bénin&rdquo; and &ldquo;Institut National des Recherche Agricoles du Benin&rdquo; and &ldquo;National Agricultural Research Institute, Benin&rdquo;</li>
<li>International Insitute of Tropical Agriculture</li>
<li>Centro Internacional de Agricultura Tropical</li>
<li>&ldquo;Rivers State University of Science and Technology&rdquo; and &ldquo;Rivers State University&rdquo;</li>
<li>&ldquo;Institut de la Recherche Agronomique, Cameroon&rdquo; and &ldquo;Institut de Recherche Agronomique, Cameroon&rdquo;</li>
<li>Inconsistency in countries: &ldquo;COTE DIVOIRE&rdquo; and &ldquo;COTE D&rsquo;IVOIRE&rdquo;</li>
<li>A few DOIs with spaces or invalid characters</li>
<li>Inconsistency in IITA subjects, for example &ldquo;PRODUCTION VEGETALE&rdquo; and &ldquo;PRODUCTION VÉGÉTALE&rdquo; and several others</li>
<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>
</ul></li>
<li>It turns out that Abenet actually did a lot of small corrections on this data so when Sisay uses Bosede&rsquo;s original file it doesn&rsquo;t have all those corrections</li>
<li>So I told Sisay to re-create the collection using Abenet&rsquo;s XLS from last week (<code>Mercy1805_AY.xls</code>)</li>
<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>
<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>
<li>I wonder if I should start checking for &ldquo;smart&rdquo; quotes like (hex 2019)</li>
</ul>
2018-06-12 09:42:43 +02:00
<h2 id="2018-06-12">2018-06-12</h2>
<ul>
<li>Udana from IWMI asked about the OAI base URL for their community on CGSpace</li>
<li>I think it should be this: <a href="https://cgspace.cgiar.org/oai/request?verb=ListRecords&amp;metadataPrefix=oai_dc&amp;set=com_10568_16814">https://cgspace.cgiar.org/oai/request?verb=ListRecords&amp;metadataPrefix=oai_dc&amp;set=com_10568_16814</a></li>
<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>
<li>Regarding Udana&rsquo;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&rsquo;d check them after that</li>
<li>The latest batch of IITA&rsquo;s 200 records (based on Abenet&rsquo;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>
<li>So here are some corrections:
<ul>
<li>use of Unicode smart quote (hex 2019) in countries and affiliations, for example &ldquo;COTE DIVOIRE&rdquo; and &ldquo;Institut dEconomic Rurale, Mali&rdquo;</li>
<li>inconsistencies in <code>cg.contributor.affiliation</code>:</li>
<li>&ldquo;Centro Internacional de Agricultura Tropical&rdquo; and &ldquo;Centro International de Agricultura Tropical&rdquo; should use the English name of CIAT (International Center for Tropical Agriculture)</li>
<li>&ldquo;Institut International d&rsquo;Agriculture Tropicale&rdquo; should use the English name of IITA (International Institute of Tropical Agriculture)</li>
<li>&ldquo;East and Southern Africa Regional Center&rdquo; and &ldquo;Eastern and Southern Africa Regional Centre&rdquo;</li>
<li>&ldquo;Institut de la Recherche Agronomique, Cameroon&rdquo; and &ldquo;Institut de Recherche Agronomique, Cameroon&rdquo;</li>
<li>&ldquo;Institut des Recherches Agricoles du Bénin&rdquo; and &ldquo;Institut National des Recherche Agricoles du Benin&rdquo; and &ldquo;National Agricultural Research Institute, Benin&rdquo;</li>
<li>&ldquo;Institute of Agronomic Research, Cameroon&rdquo; and &ldquo;Institute of Agronomy Research, Cameroon&rdquo;</li>
<li>&ldquo;Rivers State University&rdquo; and &ldquo;Rivers State University of Science and Technology&rdquo;</li>
<li>&ldquo;Universität Hannover&rdquo; and &ldquo;University of Hannover&rdquo;</li>
<li>inconsistencies in <code>cg.subject.iita</code>:</li>
<li>&ldquo;AMELIORATION DES PLANTES&rdquo; and &ldquo;AMÉLIORATION DES PLANTES&rdquo;</li>
<li>&ldquo;PRODUCTION VEGETALE&rdquo; and &ldquo;PRODUCTION VÉGÉTALE&rdquo;</li>
<li>&ldquo;CONTRÔLE DE MALADIES&rdquo; and &ldquo;CONTROLE DES MALADIES&rdquo;</li>
<li>&ldquo;HANDLING, TRANSPORT, STORAGE AND PROTECTION OF AGRICULTURAL PRODUCT&rdquo; and &ldquo;HANDLING, TRANSPORT, STORAGE AND PROTECTION OF AGRICULTURAL PRODUCTS&rdquo;</li>
<li>&ldquo;RAVAGEURS DE PLANTES&rdquo; and &ldquo;RAVAGEURS DES PLANTES&rdquo;</li>
<li>&ldquo;SANTE DES PLANTES&rdquo; and &ldquo;SANTÉ DES PLANTES&rdquo;</li>
<li>&ldquo;SOCIOECONOMIE&rdquo; and &ldquo;SOCIOECONOMY&rdquo;</li>
<li>inconsistencies in <code>dc.description.sponsorship</code>:</li>
<li>&ldquo;Belgian Corporation&rdquo; and &ldquo;Belgium Corporation&rdquo;</li>
<li>inconsistencies in <code>dc.subject</code>:</li>
<li>&ldquo;AFRICAN CASSAVA MOSAIC&rdquo; and &ldquo;AFRICAN CASSAVA MOSAIC DISEASE&rdquo;</li>
<li>&ldquo;ASPERGILLU FLAVUS&rdquo; and &ldquo;ASPERGILLUS FLAVUS&rdquo;</li>
<li>&ldquo;BIOTECHNOLOGIES&rdquo; and &ldquo;BIOTECHNOLOGY&rdquo;</li>
<li>&ldquo;CASSAVA MOSAIC DISEASE&rdquo; and &ldquo;CASSAVA MOSAIC DISEASES&rdquo; and &ldquo;CASSAVA MOSAIC VIRUS&rdquo;</li>
<li>&ldquo;CASSAVA PROCESSING&rdquo; and &ldquo;CASSAVA PROCESSING TECHNOLOGY&rdquo;</li>
<li>&ldquo;CROPPING SYSTEM&rdquo; and &ldquo;CROPPING SYSTEMS&rdquo;</li>
<li>&ldquo;DRY SEASON&rdquo; and &ldquo;DRY-SEASON&rdquo;</li>
<li>&ldquo;FERTILIZER&rdquo; and &ldquo;FERTILIZERS&rdquo;</li>
<li>&ldquo;LEGUME&rdquo; and &ldquo;LEGUMES&rdquo;</li>
<li>&ldquo;LEGUMINOSAE&rdquo; and &ldquo;LEGUMINOUS&rdquo;</li>
<li>&ldquo;LEGUMINOUS COVER CROP&rdquo; and &ldquo;LEGUMINOUS COVER CROPS&rdquo;</li>
<li>&ldquo;MATÉRIEL DE PLANTATION&rdquo; and &ldquo;MATÉRIELS DE PLANTATION&rdquo;</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&rsquo;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>
2018-06-13 08:22:58 +02:00
<li><a href="https://dspacetest.cgiar.org/10568/96113">https://dspacetest.cgiar.org/10568/96113</a></li>
2018-06-12 09:42:43 +02:00
</ul></li>
</ul>
2018-06-13 08:22:58 +02:00
<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&rsquo;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
&quot;Buruchara, Robin&quot;,Robin Buruchara: 0000-0003-0934-1218
&quot;Buruchara, Robin A.&quot;,Robin Buruchara: 0000-0003-0934-1218
</code></pre>
<ul>
<li>On a hunch I checked to see if CGSpace&rsquo;s bitstream cleanup was working properly and of course it&rsquo;s broken:</li>
</ul>
<pre><code>$ dspace cleanup -v
...
Error: ERROR: update or delete on table &quot;bitstream&quot; violates foreign key constraint &quot;bundle_primary_bitstream_id_fkey&quot; on table &quot;bundle&quot;
Detail: Key (bitstream_id)=(152402) is still referenced from table &quot;bundle&quot;.
</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>
2018-06-12 09:42:43 +02:00
<h1 id="vim-set-sw-2-ts-2">vim: set sw=2 ts=2:</h1>
2018-06-05 06:31:29 +02:00
</article>
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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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