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Update notes for 2018-02-14

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Alan Orth
2018-02-14 16:45:03 +02:00
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@ -23,7 +23,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-pl
<meta property="article:published_time" content="2018-02-01T16:28:54&#43;02:00"/>
<meta property="article:modified_time" content="2018-02-13T17:50:12&#43;02:00"/>
<meta property="article:modified_time" content="2018-02-14T13:56:18&#43;02:00"/>
@ -57,9 +57,9 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
"@type": "BlogPosting",
"headline": "February, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-02/",
"wordCount": "3297",
"wordCount": "3527",
"datePublished": "2018-02-01T16:28:54&#43;02:00",
"dateModified": "2018-02-13T17:50:12&#43;02:00",
"dateModified": "2018-02-14T13:56:18&#43;02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -667,7 +667,47 @@ $ tidy -xml -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
</code></pre>
<ul>
<li>Then it preserves them and submitting them is fine</li>
<li>This preserves special accent characters</li>
<li>I tested the display and store of these in the XMLUI and PostgreSQL and it looks good</li>
<li>Sisay exported all ILRI, CIAT, etc authors from ORCID and sent a list of 600+</li>
<li>Peter combined it with mine and we have 1204 unique ORCIDs!</li>
</ul>
<pre><code>$ grep -coE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' CGcenter_ORCID_ID_combined.csv
1204
$ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' CGcenter_ORCID_ID_combined.csv | sort | uniq | wc -l
1204
</code></pre>
<ul>
<li>Also, save that regex for the future because it will be very useful!</li>
<li>CIAT sent a list of their authors&rsquo; ORCIDs and combined with ours there are now 1227:</li>
</ul>
<pre><code>$ cat CGcenter_ORCID_ID_combined.csv ciat-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq | wc -l
1227
</code></pre>
<ul>
<li>There are some formatting issues with names in Peter&rsquo;s list, so I should remember to re-generate the list of names from ORCID&rsquo;s API once we&rsquo;re done</li>
<li>The <code>dspace cleanup -v</code> currently fails on CGSpace with the following:</li>
</ul>
<pre><code> - Deleting bitstream record from database (ID: 149473)
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)=(149473) is still referenced from table &quot;bundle&quot;.
</code></pre>
<ul>
<li>The solution is to update the bitstream table, as I&rsquo;ve discovered several other times in 2016 and 2017:</li>
</ul>
<pre><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (149473);'
UPDATE 1
</code></pre>
<ul>
<li>Then the cleanup process will continue for awhile and hit another foreign key conflict, and eventually it will complete after you manually resolve them all</li>
</ul>