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July, 2016 &middot; CGSpace Notes
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<h1 class="text-primary">July, 2016</h1>
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Posted on
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Jul 1, 2016
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<h2 id="2016-07-01:edc14796891c14dec087b4bb89c38aa9">2016-07-01</h2>
<ul>
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
<li>I think this query should find and replace all authors that have &ldquo;,&rdquo; at the end of their names:</li>
</ul>
<pre><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and text_value ~ '^.+?,$';
UPDATE 95
dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and text_value ~ '^.+?,$';
text_value
------------
(0 rows)
</code></pre>
<ul>
<li>In this case the select query was showing 95 results before the update</li>
</ul>
<h2 id="2016-07-02:edc14796891c14dec087b4bb89c38aa9">2016-07-02</h2>
<ul>
<li>Comment on DSpace Jira ticket about author lookup search text (<a href="https://jira.duraspace.org/browse/DS-2329">DS-2329</a>)</li>
</ul>
<h2 id="2016-07-04:edc14796891c14dec087b4bb89c38aa9">2016-07-04</h2>
<ul>
<li>Seems the database&rsquo;s author authority values mean nothing without the <code>authority</code> Solr core from the host where they were created!</li>
</ul>
<h2 id="2016-07-05:edc14796891c14dec087b4bb89c38aa9">2016-07-05</h2>
<ul>
<li>Amend <code>backup-solr.sh</code> script so it backs up the entire Solr folder</li>
<li>We <em>really</em> only need <code>statistics</code> and <code>authority</code> but meh</li>
<li>Fix metadata for species on DSpace Test:</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i /tmp/Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 94 -d dspacetest -u dspacetest -p 'fuuu'
</code></pre>
<ul>
<li>Will run later on CGSpace</li>
<li>A user is still having problems with Sherpa/Romeo causing crashes during the submission process when the journal is &ldquo;ungraded&rdquo;</li>
<li>I tested the <a href="https://jira.duraspace.org/browse/DS-2740">patch for DS-2740</a> that I had found last month and it seems to work</li>
<li>I will merge it to <code>5_x-prod</code></li>
</ul>
<h2 id="2016-07-06:edc14796891c14dec087b4bb89c38aa9">2016-07-06</h2>
<ul>
<li>Delete 23 blank metadata values from CGSpace:</li>
</ul>
<pre><code>cgspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
DELETE 23
</code></pre>
<ul>
<li>Complete phase three of metadata migration, for the following fields:
<ul>
<li>dc.title.jtitle → dc.source</li>
<li>dc.crsubject.crpsubject → cg.contributor.crp</li>
<li>dc.contributor.affiliation → cg.contributor.affiliation</li>
<li>dc.Species → cg.species</li>
<li>dc.srplace.subregion → cg.coverage.subregion</li>
<li>dc.contributor.corporate → dc.contributor.author</li>
<li>dc.identifier.url → cg.identifier.url</li>
<li>dc.identifier.doi → cg.identifier.doi</li>
<li>dc.identifier.googleurl → cg.identifier.googleurl</li>
<li>dc.identifier.dataurl → cg.identifier.dataurl</li>
</ul></li>
<li>Also, run fixes and deletes for species and author affiliations (over 1000 corrections!)</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 212 -d dspace -u dspace -p 'fuuu'
$ ./fix-metadata-values.py -i Affiliations-Fix-1045-Peter-Abenet.csv -f dc.contributor.affiliation -t Correct -m 211 -d dspace -u dspace -p 'fuuu'
$ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Delete-Peter-Abenet.csv -m 211 -u dspace -d dspace -p 'fuuu'
</code></pre>
<ul>
<li>I then ran all server updates and rebooted the server</li>
</ul>
<h2 id="2016-07-11:edc14796891c14dec087b4bb89c38aa9">2016-07-11</h2>
<ul>
<li>Doing some author cleanups from Peter and Abenet:</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i /tmp/Authors-Fix-205-UTF8.csv -f dc.contributor.author -t correct -m 3 -d dspacetest -u dspacetest -p fuuu
$ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu
</code></pre>
<h2 id="2016-07-13:edc14796891c14dec087b4bb89c38aa9">2016-07-13</h2>
<ul>
<li>Run the author cleanups on CGSpace and start a full Discovery re-index</li>
</ul>
<h2 id="2016-07-18:edc14796891c14dec087b4bb89c38aa9">2016-07-18</h2>
<ul>
<li>Adjust identifiers in XMLUI item display to be more prominent</li>
<li>Add species and breed to the XMLUI item display</li>
<li>CGSpace crashed late at night and the DSpace logs were showing:</li>
</ul>
<pre><code>2016-07-18 20:26:30,941 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
...
</code></pre>
<ul>
<li>I suspect it&rsquo;s someone hitting REST too much:</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3
710 66.249.78.38
1781 181.118.144.29
24904 70.32.99.142
</code></pre>
<ul>
<li>I just blocked access to <code>/rest</code> for that last IP for now:</li>
</ul>
<pre><code> # log rest requests
location /rest {
access_log /var/log/nginx/rest.log;
proxy_pass http://127.0.0.1:8443;
deny 70.32.99.142;
}
</code></pre>
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