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<meta property="og:title" content=" April, 2016 · CGSpace Notes" />
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April, 2016 · CGSpace Notes
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<header class="global-header" style="background-image:url(../images/bg.jpg )">
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<section class="header-text">
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<h1><a href="/cgspace-notes/">CGSpace Notes</a></h1>
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<h1><a href="https://alanorth.github.io/cgspace-notes/">CGSpace Notes</a></h1>
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<span class="post-tag small"><a href="/cgspace-notes//tags/notes">#notes</a></span>
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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="2016-04-04:c88be15f5b2f07c85f7742556a955e47">2016-04-04</h2>
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<h2 id="2016-04-04">2016-04-04</h2>
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<ul>
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<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
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@ -120,7 +120,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290
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<li>Submit pull request for Tomcat 7 limits in Ansible dspace role (<a href="https://github.com/ilri/rmg-ansible-public/pull/30">#30</a>)</li>
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</ul>
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<h2 id="2016-04-05:c88be15f5b2f07c85f7742556a955e47">2016-04-05</h2>
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<h2 id="2016-04-05">2016-04-05</h2>
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<ul>
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<li>Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don’t need!</li>
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@ -138,7 +138,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290
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<li>Try to do some metadata field migrations using the Atmire batch UI (<code>dc.Species</code> → <code>cg.species</code>) but it took several hours and even missed a few records</li>
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</ul>
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<h2 id="2016-04-06:c88be15f5b2f07c85f7742556a955e47">2016-04-06</h2>
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<h2 id="2016-04-06">2016-04-06</h2>
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<ul>
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<li>A better way to move metadata on this scale is via SQL, for example <code>dc.type.output</code> → <code>dc.type</code> (their IDs in the metadatafieldregistry are 66 and 109, respectively):</li>
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@ -153,7 +153,7 @@ UPDATE 40852
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<li>Start working on metadata migrations, add 25 or so new metadata fields to CGSpace</li>
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</ul>
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<h2 id="2016-04-07:c88be15f5b2f07c85f7742556a955e47">2016-04-07</h2>
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<h2 id="2016-04-07">2016-04-07</h2>
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<ul>
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<li>Write shell script to do the migration of fields: <a href="https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b">https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b</a></li>
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@ -169,14 +169,14 @@ UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
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UPDATE 51258
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</code></pre>
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<h2 id="2016-04-08:c88be15f5b2f07c85f7742556a955e47">2016-04-08</h2>
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<h2 id="2016-04-08">2016-04-08</h2>
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<ul>
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<li>Discuss metadata renaming with Abenet, we decided it’s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF</li>
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<li>I’ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change</li>
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</ul>
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<h2 id="2016-04-10:c88be15f5b2f07c85f7742556a955e47">2016-04-10</h2>
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<h2 id="2016-04-10">2016-04-10</h2>
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<ul>
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<li>Looking at the DOI issue <a href="https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=678507860">reported by Leroy from CIAT a few weeks ago</a></li>
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@ -199,14 +199,14 @@ dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and t
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<li>I will manually edit the <code>dc.identifier.doi</code> in <a href="https://cgspace.cgiar.org/handle/10568/72509?show=full"><sup>10568</sup>⁄<sub>72509</sub></a> and tweet the link, then check back in a week to see if the donut gets updated</li>
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</ul>
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<h2 id="2016-04-11:c88be15f5b2f07c85f7742556a955e47">2016-04-11</h2>
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<h2 id="2016-04-11">2016-04-11</h2>
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<ul>
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<li>The donut is already updated and shows the correct number now</li>
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<li>CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we’d do it tentatively on Monday the 18th.</li>
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</ul>
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<h2 id="2016-04-12:c88be15f5b2f07c85f7742556a955e47">2016-04-12</h2>
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<h2 id="2016-04-12">2016-04-12</h2>
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<ul>
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<li>Looking at quality of WLE data (<code>cg.subject.iwmi</code>) in SQL:</li>
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@ -243,7 +243,7 @@ DELETE 226
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<li>We want to do the <code>dc.type.output</code> move on CGSpace anyways, but we should wait as it might affect other external people!</li>
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</ul>
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<h2 id="2016-04-14:c88be15f5b2f07c85f7742556a955e47">2016-04-14</h2>
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<h2 id="2016-04-14">2016-04-14</h2>
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<ul>
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<li>Communicate with Macaroni Bros again about <code>dc.type</code></li>
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@ -251,13 +251,13 @@ DELETE 226
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<li>Notify CIAT people of metadata changes (I had forgotten them last week)</li>
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</ul>
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<h2 id="2016-04-15:c88be15f5b2f07c85f7742556a955e47">2016-04-15</h2>
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<h2 id="2016-04-15">2016-04-15</h2>
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<ul>
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<li>DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code</li>
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</ul>
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<h2 id="2016-04-18:c88be15f5b2f07c85f7742556a955e47">2016-04-18</h2>
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<h2 id="2016-04-18">2016-04-18</h2>
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<ul>
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<li>Talk to CIAT people about their portal again</li>
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<li>After restarting Tomcat a few more of these errors were logged but the application was up</li>
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</ul>
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<h2 id="2016-04-19:c88be15f5b2f07c85f7742556a955e47">2016-04-19</h2>
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<h2 id="2016-04-19">2016-04-19</h2>
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<ul>
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<li>Get handles for items that are using a given metadata field, ie <code>dc.Species.animal</code> (105):</li>
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<li>And then remove them from the metadata registry</li>
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</ul>
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<h2 id="2016-04-20:c88be15f5b2f07c85f7742556a955e47">2016-04-20</h2>
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<h2 id="2016-04-20">2016-04-20</h2>
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<ul>
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<li>Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server</li>
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<li>I’ve sent a message to Atmire asking about compatibility with DSpace 5.5</li>
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</ul>
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<h2 id="2016-04-21:c88be15f5b2f07c85f7742556a955e47">2016-04-21</h2>
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<h2 id="2016-04-21">2016-04-21</h2>
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<ul>
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<li>Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)</li>
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<li>Atmire responded with DSpace 5.5 compatible versions for their modules, so I’ll start testing those in a few weeks</li>
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</ul>
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<h2 id="2016-04-22:c88be15f5b2f07c85f7742556a955e47">2016-04-22</h2>
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<h2 id="2016-04-22">2016-04-22</h2>
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<ul>
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<li>Import 95 records into <a href="https://cgspace.cgiar.org/handle/10568/42219">CTA’s Agrodok collection</a></li>
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</ul>
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<h2 id="2016-04-26:c88be15f5b2f07c85f7742556a955e47">2016-04-26</h2>
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<h2 id="2016-04-26">2016-04-26</h2>
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<ul>
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<li>Test embargo during item upload</li>
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@ -460,7 +460,7 @@ UPDATE 46075
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</ul></li>
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</ul>
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<h2 id="2016-04-27:c88be15f5b2f07c85f7742556a955e47">2016-04-27</h2>
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<h2 id="2016-04-27">2016-04-27</h2>
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<ul>
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<li>I woke up to ten or fifteen “up” and “down” emails from the monitoring website</li>
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@ -507,14 +507,14 @@ dspace.log.2016-04-27:7271
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<li>CGSpace down, restarted tomcat and it’s back up</li>
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</ul>
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<h2 id="2016-04-28:c88be15f5b2f07c85f7742556a955e47">2016-04-28</h2>
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<h2 id="2016-04-28">2016-04-28</h2>
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<ul>
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<li>Problems with stability again. I’ve blocked access to <code>/rest</code> for now to see if the number of errors in the log files drop</li>
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<li>Later we could maybe start logging access to <code>/rest</code> and perhaps whitelist some IPs…</li>
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</ul>
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<h2 id="2016-04-30:c88be15f5b2f07c85f7742556a955e47">2016-04-30</h2>
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<h2 id="2016-04-30">2016-04-30</h2>
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<ul>
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<li>Logs for today and yesterday have zero references to this REST error, so I’m going to open back up the REST API but log all requests</li>
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