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February, 2016 · CGSpace Notes
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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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<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
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<ul>
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<li>Re-sync DSpace Test with CGSpace</li>
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<li>Help Sisay with OpenRefine</li>
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<li>Enable HTTPS on DSpace Test using Let’s Encrypt:</li>
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</ul>
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<pre><code>$ cd ~/src/git
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$ git clone https://github.com/letsencrypt/letsencrypt
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$ cd letsencrypt
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$ sudo service nginx stop
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# add port 443 to firewall rules
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$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
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$ sudo service nginx start
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$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
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</code></pre>
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<ul>
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<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
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<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs…</li>
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<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li>
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<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
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<li>Logs don’t always show anything right when it fails, but eventually one of these appears:</li>
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</ul>
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<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>or</li>
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</ul>
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<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
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</code></pre>
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<ul>
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<li>Right now DSpace Test’s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
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</ul>
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<pre><code># free -m
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total used free shared buffers cached
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Mem: 3950 3902 48 9 37 1311
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-/+ buffers/cache: 2552 1397
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Swap: 255 57 198
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</code></pre>
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<ul>
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<li>So I’ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
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</ul>
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<h2 id="2016-02-11:124a59adbaa8ef13e1518d003fc03981">2016-02-11</h2>
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<ul>
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<li>Massaging some CIAT data in OpenRefine</li>
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<li>There are 1200 records that have PDFs, and will need to be imported into CGSpace</li>
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<li>I created a <code>filename</code> column based on the <code>dc.identifier.url</code> column using the following transform:</li>
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</ul>
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<pre><code>value.split('/')[-1]
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</code></pre>
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<ul>
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<li>Then I wrote a tool called <a href="https://gist.github.com/alanorth/2206f24483fe5f0454fc"><code>generate-thumbnails.py</code></a> to download the PDFs and generate thumbnails for them, for example:</li>
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</ul>
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<pre><code>$ ./generate-thumbnails.py ciat-reports.csv
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Processing 64661.pdf
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> Downloading 64661.pdf
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> Creating thumbnail for 64661.pdf
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Processing 64195.pdf
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> Downloading 64195.pdf
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> Creating thumbnail for 64195.pdf
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</code></pre>
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<h2 id="2016-02-12:124a59adbaa8ef13e1518d003fc03981">2016-02-12</h2>
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<ul>
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<li>Looking at CIAT’s records again, there are some problems with a dozen or so files (out of 1200)</li>
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<li>A few items are using the same exact PDF</li>
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<li>A few items are using HTM or DOC files</li>
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<li>A few items link to PDFs on IFPRI’s e-Library or Research Gate</li>
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<li>A few items have no item</li>
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<li>Also, I’m not sure if we import these items, will be remove the <code>dc.identifier.url</code> field from the records?</li>
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</ul>
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<h2 id="2016-02-12-1:124a59adbaa8ef13e1518d003fc03981">2016-02-12</h2>
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<ul>
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<li>Looking at CIAT’s records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I’m not sure if we can use those</li>
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<li>265 items have dirty, URL-encoded filenames:</li>
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</ul>
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<pre><code>$ ls | grep -c -E "%"
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265
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</code></pre>
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<ul>
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<li>I suggest that we import ~850 or so of the clean ones first, then do the rest after I can find a clean/reliable way to decode the filenames</li>
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<li>This python2 snippet seems to work in the CLI, but not so well in OpenRefine:</li>
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</ul>
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<pre><code>$ python -c "import urllib, sys; print urllib.unquote(sys.argv[1])" CIAT_COLOMBIA_000169_T%C3%A9cnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_yuca.pdf
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CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_yuca.pdf
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</code></pre>
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<ul>
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<li>Merge pull requests for submission form theming (<a href="https://github.com/ilri/DSpace/pull/178">#178</a>) and missing center subjects in XMLUI item views (<a href="https://github.com/ilri/DSpace/pull/176">#176</a>)</li>
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<li>They will be deployed on CGSpace the next time I re-deploy</li>
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<h1 class="author-name text-primary">Alan Orth</h1>
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