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<meta property="og:title" content=" February, 2016 · CGSpace Notes" />
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February, 2016 · CGSpace Notes
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<header class="global-header" style="background-image:url(../images/bg.jpg )">
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<h1 class="text-primary">February, 2016</h1>
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Posted on
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<time datetime="2016-02-05T13:18:00+03:00">
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Feb 5, 2016
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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<section>
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<h2 id="2016-02-05:124a59adbaa8ef13e1518d003fc03981">2016-02-05</h2>
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<ul>
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<li>Looking at some DAGRIS data for Abenet Yabowork</li>
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<li>Lots of issues with spaces, newlines, etc causing the import to fail</li>
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<li>I noticed we have a very <em>interesting</em> list of countries on CGSpace:</li>
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</ul>
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<p><img src="../images/2016/02/cgspace-countries.png" alt="CGSpace country list" /></p>
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<ul>
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<li>Not only are there 49,000 countries, we have some blanks (25)…</li>
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<li>Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”</li>
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</ul>
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<h2 id="2016-02-06:124a59adbaa8ef13e1518d003fc03981">2016-02-06</h2>
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<ul>
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<li>Found a way to get items with null/empty metadata values from SQL</li>
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<li>First, find the <code>metadata_field_id</code> for the field you want from the <code>metadatafieldregistry</code> table:</li>
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</ul>
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<pre><code>dspacetest=# select * from metadatafieldregistry;
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</code></pre>
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<ul>
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<li>In this case our country field is 78</li>
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<li>Now find all resources with type 2 (item) that have null/empty values for that field:</li>
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</ul>
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<pre><code>dspacetest=# select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=78 and (text_value='' OR text_value IS NULL);
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</code></pre>
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<ul>
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<li>Then you can find the handle that owns it from its <code>resource_id</code>:</li>
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</ul>
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<pre><code>dspacetest=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id = '22678';
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</code></pre>
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<ul>
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<li>It’s 25 items so editing in the web UI is annoying, let’s try SQL!</li>
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</ul>
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<pre><code>dspacetest=# delete from metadatavalue where metadata_field_id=78 and text_value='';
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DELETE 25
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</code></pre>
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<ul>
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<li>After that perhaps a regular <code>dspace index-discovery</code> (no -b) <em>should</em> suffice…</li>
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<li>Hmm, I indexed, cleared the Cocoon cache, and restarted Tomcat but the 25 “|||” countries are still there</li>
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<li>Maybe I need to do a full re-index…</li>
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<li>Yep! The full re-index seems to work.</li>
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<li>Process the empty countries on CGSpace</li>
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</ul>
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<h2 id="2016-02-07:124a59adbaa8ef13e1518d003fc03981">2016-02-07</h2>
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<ul>
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<li>Working on cleaning up Abenet’s DAGRIS data with OpenRefine</li>
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<li>I discovered two really nice functions in OpenRefine: <code>value.trim()</code> and <code>value.escape("javascript")</code> which shows whitespace characters like <code>\r\n</code>!</li>
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<li>For some reason when you import an Excel file into OpenRefine it exports dates like 1949 to 1949.0 in the CSV</li>
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<li>I re-import the resulting CSV and run a GREL on the date issued column: <code>value.replace("\.0", "")</code></li>
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<li>I need to start running DSpace in Mac OS X instead of a Linux VM</li>
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<li>Install PostgreSQL from homebrew, then configure and import CGSpace database dump:</li>
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</ul>
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<pre><code>$ postgres -D /opt/brew/var/postgres
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$ createuser --superuser postgres
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$ createuser --pwprompt dspacetest
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$ createdb -O dspacetest --encoding=UNICODE dspacetest
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$ psql postgres
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postgres=# alter user dspacetest createuser;
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postgres=# \q
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$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-02-07.backup
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$ psql postgres
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postgres=# alter user dspacetest nocreateuser;
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postgres=# \q
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$ vacuumdb dspacetest
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$ psql -U dspacetest -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest -h localhost
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</code></pre>
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<ul>
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<li>After building and running a <code>fresh_install</code> I symlinked the webapps into Tomcat’s webapps folder:</li>
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</ul>
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<pre><code>$ mv /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT.orig
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$ ln -sfv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT
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$ ln -sfv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/rest
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$ ln -sfv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/jspui
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$ ln -sfv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/oai
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$ ln -sfv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/solr
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$ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
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</code></pre>
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<ul>
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<li>Add CATALINA_OPTS in <code>/opt/brew/Cellar/tomcat/8.0.30/libexec/bin/setenv.sh</code>, as this script is sourced by the <code>catalina</code> startup script</li>
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<li>For example:</li>
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</ul>
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<pre><code>CATALINA_OPTS="-Djava.awt.headless=true -Xms2048m -Xmx2048m -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8"
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</code></pre>
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<ul>
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<li>After verifying that the site is working, start a full index:</li>
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</ul>
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<pre><code>$ ~/dspace/bin/dspace index-discovery -b
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</code></pre>
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<h2 id="2016-02-08:124a59adbaa8ef13e1518d003fc03981">2016-02-08</h2>
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<ul>
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<li>Finish cleaning up and importing ~400 DAGRIS items into CGSpace</li>
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<li>Whip up some quick CSS to make the button in the submission workflow use the XMLUI theme’s brand colors (<a href="https://github.com/ilri/DSpace/issues/154">#154</a>)</li>
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</ul>
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<p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
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<img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
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<h1 class="author-name text-primary">Alan Orth</h1>
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