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July, 2016 · CGSpace Notes
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<h1><a href="https://alanorth.github.io/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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<time datetime="2016-07-01T10:53:00+03:00">
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Jul 1, 2016
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<span class="post-tag small"><a href="https://alanorth.github.io/cgspace-notes//tags/notes">#notes</a></span>
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<section>
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<h2 id="2016-07-01">2016-07-01</h2>
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<ul>
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<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>
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<li>I think this query should find and replace all authors that have “,” at the end of their names:</li>
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</ul>
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<pre><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and text_value ~ '^.+?,$';
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UPDATE 95
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dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and text_value ~ '^.+?,$';
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text_value
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------------
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(0 rows)
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</code></pre>
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<ul>
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<li>In this case the select query was showing 95 results before the update</li>
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</ul>
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<h2 id="2016-07-02">2016-07-02</h2>
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<ul>
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<li>Comment on DSpace Jira ticket about author lookup search text (<a href="https://jira.duraspace.org/browse/DS-2329">DS-2329</a>)</li>
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</ul>
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<h2 id="2016-07-04">2016-07-04</h2>
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<ul>
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<li>Seems the database’s author authority values mean nothing without the <code>authority</code> Solr core from the host where they were created!</li>
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</ul>
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<h2 id="2016-07-05">2016-07-05</h2>
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<ul>
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<li>Amend <code>backup-solr.sh</code> script so it backs up the entire Solr folder</li>
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<li>We <em>really</em> only need <code>statistics</code> and <code>authority</code> but meh</li>
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<li>Fix metadata for species on DSpace Test:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 94 -d dspacetest -u dspacetest -p 'fuuu'
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</code></pre>
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<ul>
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<li>Will run later on CGSpace</li>
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<li>A user is still having problems with Sherpa/Romeo causing crashes during the submission process when the journal is “ungraded”</li>
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<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>
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<li>I will merge it to <code>5_x-prod</code></li>
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</ul>
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<h2 id="2016-07-06">2016-07-06</h2>
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<ul>
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<li>Delete 23 blank metadata values from CGSpace:</li>
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</ul>
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<pre><code>cgspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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DELETE 23
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</code></pre>
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<ul>
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<li>Complete phase three of metadata migration, for the following fields:
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<ul>
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<li>dc.title.jtitle → dc.source</li>
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<li>dc.crsubject.crpsubject → cg.contributor.crp</li>
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<li>dc.contributor.affiliation → cg.contributor.affiliation</li>
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<li>dc.Species → cg.species</li>
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<li>dc.srplace.subregion → cg.coverage.subregion</li>
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<li>dc.contributor.corporate → dc.contributor.author</li>
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<li>dc.identifier.url → cg.identifier.url</li>
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<li>dc.identifier.doi → cg.identifier.doi</li>
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<li>dc.identifier.googleurl → cg.identifier.googleurl</li>
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<li>dc.identifier.dataurl → cg.identifier.dataurl</li>
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</ul></li>
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<li>Also, run fixes and deletes for species and author affiliations (over 1000 corrections!)</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 212 -d dspace -u dspace -p 'fuuu'
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$ ./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'
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$ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Delete-Peter-Abenet.csv -m 211 -u dspace -d dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>I then ran all server updates and rebooted the server</li>
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</ul>
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<h2 id="2016-07-11">2016-07-11</h2>
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<ul>
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<li>Doing some author cleanups from Peter and Abenet:</li>
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</ul>
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<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
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$ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu
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</code></pre>
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<h2 id="2016-07-13">2016-07-13</h2>
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<ul>
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<li>Run the author cleanups on CGSpace and start a full Discovery re-index</li>
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</ul>
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<h2 id="2016-07-14">2016-07-14</h2>
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<ul>
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<li>Test LDAP settings for new root LDAP</li>
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<li>Seems to work when binding as a top-level user</li>
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</ul>
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<h2 id="2016-07-18">2016-07-18</h2>
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<ul>
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<li>Adjust identifiers in XMLUI item display to be more prominent</li>
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<li>Add species and breed to the XMLUI item display</li>
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<li>CGSpace crashed late at night and the DSpace logs were showing:</li>
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</ul>
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<pre><code>2016-07-18 20:26:30,941 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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...
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</code></pre>
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<ul>
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<li>I suspect it’s someone hitting REST too much:</li>
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</ul>
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<pre><code># awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3
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710 66.249.78.38
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1781 181.118.144.29
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24904 70.32.99.142
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</code></pre>
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<ul>
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<li>I just blocked access to <code>/rest</code> for that last IP for now:</li>
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</ul>
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<pre><code> # log rest requests
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location /rest {
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access_log /var/log/nginx/rest.log;
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proxy_pass http://127.0.0.1:8443;
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deny 70.32.99.142;
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}
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</code></pre>
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<h2 id="2016-07-21">2016-07-21</h2>
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<ul>
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<li>Mitigate the <a href="https://httpoxy.org">HTTPoxy</a> vulnerability for Tomcat etc in nginx: <a href="https://github.com/ilri/rmg-ansible-public/pull/38">https://github.com/ilri/rmg-ansible-public/pull/38</a></li>
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<li>Unblock 70.32.99.142 from <code>/rest</code> as it has been blocked for a few days</li>
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</ul>
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<h2 id="2016-07-22">2016-07-22</h2>
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<ul>
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<li>Help Paola from CCAFS with thumbnails for batch uploads</li>
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<li>She has been struggling to get the dimensions right, and manually enlarging smaller thumbnails, renaming PNGs to JPG, etc</li>
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<li>Altmetric reports having an issue with some of our authors being doubled…</li>
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<li>This is related to authority and confidence!</li>
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<li>We might need to use <code>index.authority.ignore-prefered=true</code> to tell the Discovery index to prefer the variation that exists in the metadatavalue rather than what it finds in the authority cache.</li>
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<li>Trying these on DSpace Test after a discussion by Daniel Scharon on the dspace-tech mailing list:</li>
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</ul>
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<pre><code>index.authority.ignore-prefered.dc.contributor.author=true
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index.authority.ignore-variants.dc.contributor.author=false
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</code></pre>
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<ul>
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<li>After reindexing I don’t see any change in Discovery’s display of authors, and still have entries like:</li>
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</ul>
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<pre><code>Grace, D. (464)
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Grace, D. (62)
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</code></pre>
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<ul>
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<li>I asked for clarification of the following options on the DSpace mailing list:</li>
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</ul>
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<pre><code>index.authority.ignore
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index.authority.ignore-prefered
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index.authority.ignore-variants
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</code></pre>
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<ul>
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<li>In the mean time, I will try these on DSpace Test (plus a reindex):</li>
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</ul>
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<pre><code>index.authority.ignore=true
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index.authority.ignore-prefered=true
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index.authority.ignore-variants=true
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</code></pre>
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<ul>
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<li>Enabled usage of <code>X-Forwarded-For</code> in DSpace admin control panel (<a href="https://github.com/ilri/DSpace/pull/255">#255</a></li>
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<li>It was misconfigured and disabled, but already working for some reason <em>sigh</em></li>
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<li>… no luck. Trying with just:</li>
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</ul>
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<pre><code>index.authority.ignore=true
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</code></pre>
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<ul>
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<li>After re-indexing and clearing the XMLUI cache nothing has changed</li>
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</ul>
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<h2 id="2016-07-25">2016-07-25</h2>
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<ul>
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<li>Trying a few more settings (plus reindex) for Discovery on DSpace Test:</li>
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</ul>
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<pre><code>index.authority.ignore-prefered.dc.contributor.author=true
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index.authority.ignore-variants=true
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</code></pre>
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<ul>
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<li>Run all OS updates and reboot DSpace Test server</li>
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<li>No changes to Discovery after reindexing… hmm.</li>
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<li>Integrate and massively clean up About page (<a href="https://github.com/ilri/DSpace/pull/256">#256</a>)</li>
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</ul>
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<p><img src="../images/2016/07/cgspace-about-page.png" alt="About page" /></p>
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<ul>
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<li>The DSpace source code mentions the configuration key <code>discovery.index.authority.ignore-prefered.*</code> (with prefix of discovery, despite the docs saying otherwise), so I’m trying the following on DSpace Test:</li>
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</ul>
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<pre><code>discovery.index.authority.ignore-prefered.dc.contributor.author=true
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discovery.index.authority.ignore-variants=true
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</code></pre>
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<ul>
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<li>Still no change!</li>
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<li>Deploy species, breed, and identifier changes to CGSpace, as well as About page</li>
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<li>Run Linode RAM upgrade (8→12GB)</li>
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<li>Re-sync DSpace Test with CGSpace</li>
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<li>I noticed that our backup scripts don’t send Solr cores to S3 so I amended the script</li>
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</ul>
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<h2 id="2016-07-31">2016-07-31</h2>
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<ul>
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<li>Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by</li>
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<li>Also change “Subjects” to “AGROVOC keywords” in Discovery sidebar/search and Browse by (<a href="https://github.com/ilri/DSpace/issues/257">#257</a>)</li>
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<h1 class="author-name text-primary">Alan Orth</h1>
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