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Add notes for 2019-12-17
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@ -43,7 +43,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did
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The server only has 8GB of RAM so we'll eventually need to upgrade to a larger one because we'll start starving the OS, PostgreSQL, and command line batch processes
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I ran all system updates on DSpace Test and rebooted it
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"/>
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<meta name="generator" content="Hugo 0.60.1" />
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<meta name="generator" content="Hugo 0.61.0" />
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@ -124,7 +124,7 @@ I ran all system updates on DSpace Test and rebooted it
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</p>
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</header>
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<h2 id="20180801">2018-08-01</h2>
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<h2 id="2018-08-01">2018-08-01</h2>
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<ul>
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<li>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</li>
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</ul>
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@ -149,7 +149,7 @@ I ran all system updates on DSpace Test and rebooted it
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</ul>
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</li>
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</ul>
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<h2 id="20180802">2018-08-02</h2>
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<h2 id="2018-08-02">2018-08-02</h2>
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<ul>
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<li>DSpace Test crashed again and I don't see the only error I see is this in <code>dmesg</code>:</li>
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</ul>
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@ -165,7 +165,7 @@ I ran all system updates on DSpace Test and rebooted it
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<li>I just tried to enable the stats again on DSpace Test now that we're on DSpace 5.8 with updated Atmire modules, but every user I search for shows “No data available”</li>
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<li>As a test I submitted a new item and I was able to see it in the workflow statistics “data” tab, but not in the graph</li>
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</ul>
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<h2 id="20180815">2018-08-15</h2>
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<h2 id="2018-08-15">2018-08-15</h2>
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<ul>
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<li>Run through Peter's list of author affiliations from earlier this month</li>
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<li>I did some quick sanity checks and small cleanups in Open Refine, checking for spaces, weird accents, and encoding errors</li>
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@ -173,7 +173,7 @@ I ran all system updates on DSpace Test and rebooted it
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i 2018-08-15-Correct-1083-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t correct -m 211
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$ ./delete-metadata-values.py -i 2018-08-15-Remove-11-Affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
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</code></pre><h2 id="20180816">2018-08-16</h2>
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</code></pre><h2 id="2018-08-16">2018-08-16</h2>
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<ul>
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<li>Generate a list of the top 1,500 authors on CGSpace for Sisay so he can create the controlled vocabulary:</li>
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</ul>
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@ -194,7 +194,7 @@ $ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest superuser;'
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$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest ~/Downloads/cgspace_2018-08-16.backup
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$ psql -h localhost -U postgres dspacetest -c 'alter user dspacetest nosuperuser;'
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$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
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</code></pre><h2 id="20180819">2018-08-19</h2>
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</code></pre><h2 id="2018-08-19">2018-08-19</h2>
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<ul>
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<li>Keep working on the CIAT ORCID identifiers from Elizabeth</li>
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<li>In the spreadsheet she sent me there are some names with other versions in the database, so when it is obviously the same one (ie “Schultze-Kraft, Rainer” and “Schultze-Kraft, R.") I will just tag them with ORCID identifiers too</li>
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@ -296,7 +296,7 @@ sys 2m20.248s
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</code></pre><ul>
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<li>So I'm thinking we should add “crawl” to the Tomcat Crawler Session Manager valve, as we already have “bot” that catches Googlebot, Bingbot, etc.</li>
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</ul>
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<h2 id="20180820">2018-08-20</h2>
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<h2 id="2018-08-20">2018-08-20</h2>
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<ul>
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<li>Help Sisay with some UTF-8 encoding issues in a file Peter sent him</li>
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<li>Finish up reconciling Atmire's pull request for DSpace 5.8 changes with the latest status of our <code>5_x-prod</code> branch</li>
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@ -313,7 +313,7 @@ sys 2m20.248s
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<li>Instead, I will archive the current <code>5_x-prod</code> DSpace 5.5 branch as <code>5_x-prod-dspace-5.5</code> and then hard reset <code>5_x-prod</code> based on <code>5_x-dspace-5.8</code></li>
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<li>Unfortunately this will mess up the references in pull requests and issues on GitHub</li>
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</ul>
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<h2 id="20180821">2018-08-21</h2>
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<h2 id="2018-08-21">2018-08-21</h2>
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<ul>
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<li>Something must have happened, as the <code>mvn package</code> <em>always</em> takes about two hours now, stopping for a very long time near the end at this step:</li>
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</ul>
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@ -335,7 +335,7 @@ sys 2m20.248s
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<li>I need to test to see if this has any side effects when deployed…</li>
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<li>In other news, I see there was a pull request in DSpace 5.9 that fixes the issue with not being able to have blank lines in CSVs when importing via command line or webui (<a href="https://jira.duraspace.org/browse/DS-3245">DS-3245</a>)</li>
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</ul>
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<h2 id="20180823">2018-08-23</h2>
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<h2 id="2018-08-23">2018-08-23</h2>
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<ul>
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<li>Skype meeting with CKM people to meet new web dev guy Tariku</li>
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<li>They say they want to start working on the ContentDM harvester middleware again</li>
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@ -345,7 +345,7 @@ sys 2m20.248s
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<li>I imported the CTA items on CGSpace for Sisay:</li>
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</ul>
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<pre><code>$ dspace import -a -e s.webshet@cgiar.org -s /home/swebshet/ictupdates_uploads_August_21 -m /tmp/2018-08-23-cta-ictupdates.map
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</code></pre><h2 id="20180826">2018-08-26</h2>
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</code></pre><h2 id="2018-08-26">2018-08-26</h2>
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<ul>
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<li>Doing the DSpace 5.8 upgrade on CGSpace (linode18)</li>
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<li>I already finished the Maven build, now I'll take a backup of the PostgreSQL database and do a database cleanup just in case:</li>
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@ -401,14 +401,14 @@ $ dspace database migrate ignored
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<li>I just checked to see if the Listings and Reports issue with using the CGSpace citation field was fixed as planned alongside the DSpace 5.8 upgrades (<a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=589">#589</a></li>
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<li>I was able to create a new layout containing only the citation field, so I closed the ticket</li>
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</ul>
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<h2 id="20180829">2018-08-29</h2>
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<h2 id="2018-08-29">2018-08-29</h2>
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<ul>
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<li>Discuss <a href="https://copo-project.org/copo/">COPO</a> with Martin Mueller</li>
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<li>He and the consortium's idea is to use this for metadata annotation (submission?) to all repositories</li>
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<li>It is somehow related to adding events as items in the repository, and then linking related papers, presentations, etc to the event item using <code>dc.relation</code>, etc.</li>
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<li>Discuss Linode server charges with Abenet, apparently we want to start charging these to Big Data</li>
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</ul>
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<h2 id="20180830">2018-08-30</h2>
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<h2 id="2018-08-30">2018-08-30</h2>
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<ul>
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<li>I fixed the graphical glitch in the cookieconsent popup (the dismiss bug is still there) by pinning the last known good version (3.0.6) in <code>bower.json</code> of each XMLUI theme</li>
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<li>I guess cookieconsent got updated without me realizing it and the previous expression <code>^3.0.6</code> make bower install version 3.1.0</li>
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