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<meta property="og:title" content="November, 2023" />
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<meta property="og:description" content="2023-11-01
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Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
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I improved the filtering and wrote some Python using pandas to merge my sources more reliably
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2023-11-02
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Export CGSpace to check missing Initiative collection mappings
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Start a harvest on AReS
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" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="November, 2023"/>
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<meta name="twitter:description" content="2023-11-01
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Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
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I improved the filtering and wrote some Python using pandas to merge my sources more reliably
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2023-11-02
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Export CGSpace to check missing Initiative collection mappings
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Start a harvest on AReS
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"/>
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-11/">November, 2023</a></h2>
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<p class="blog-post-meta">
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<time datetime="2023-11-02T12:59:36+03:00">Thu Nov 02, 2023</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2023-11-01">2023-11-01</h2>
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<ul>
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<li>Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
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<ul>
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<li>I improved the filtering and wrote some Python using pandas to merge my sources more reliably</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-11-02">2023-11-02</h2>
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<ul>
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<li>Export CGSpace to check missing Initiative collection mappings</li>
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<li>Start a harvest on AReS</li>
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</ul>
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<ul>
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<li>IFPRI contacted us about importing their Slideshare presentations to CGSpace
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<ul>
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<li>There are ~1,700 of them and date back to as early as 2008</li>
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<li>I did a quick cleanup of the metadata export from Slideshare (including tagging with some AGROVOC in OpenRefine) and uploaded to DSpace Test</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-11-03">2023-11-03</h2>
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<ul>
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<li>A little bit of work on the CGIAR Climate Change Synthesis</li>
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<li>Discuss some CGSpace migration plans with Leigh from IFPRI
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<ul>
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<li>For their Slideshare content we agreed:
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<ul>
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<li>Exclude private</li>
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<li>Exclude deleted</li>
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<li>Exclude non presentation types</li>
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<li>Exclude duplicates within the collection for now until we can sort them out</li>
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</ul>
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</li>
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<li>That leaves about 1,500 items out of the 1,700</li>
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</ul>
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</li>
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<li>I did a duplicate check against CGSpace and found 44 items with 1.0 similarity so I removed those</li>
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</ul>
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<h2 id="2023-11-04">2023-11-04</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative collection mappings</li>
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<li>I ran through the list of potential duplicates on the IFPRI Slideshare presentations</li>
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</ul>
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<h2 id="2023-11-05">2023-11-05</h2>
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<ul>
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<li>Work with Salem to migrate AReS to the new version</li>
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</ul>
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<h2 id="2023-11-07">2023-11-07</h2>
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<ul>
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<li>DSpace 7 Test went down and there is very high load on the server
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<ul>
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<li>I saw very high load from Java but didn’t have time to check exactly what was wrong so I just rebooted the host</li>
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<li>A few hours after restarting the system went down again, with very high load from Java again</li>
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<li>I see lots of messages like this in the Tomcat log:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>tomcat9[732]: [9955.662s][info ][gc] GC(6291) Pause Full (G1 Compaction Pause) 4085M->4080M(4096M) 677.251ms
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tomcat9[732]: [9955.662s][info ][gc] GC(6290) Concurrent Mark Cycle 677.558ms
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tomcat9[732]: [9955.666s][info ][gc] GC(6292) To-space exhausted
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</code></pre><ul>
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<li>I see some messages in <code>dspace.log</code> about heap space:</li>
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</ul>
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<pre tabindex="0"><code>Caused by: java.lang.OutOfMemoryError: Java heap space
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</code></pre><ul>
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<li>I will increase Tomcat’s heap from 4096m to 5120m
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<ul>
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<li>A few hours later it happened again, so I increased the heap from 5120m to 6144m</li>
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<li>Not sure what’s going on today…</li>
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</ul>
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</li>
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<li>I tested moving the CGIAR Fund Council community to the CGIAR historic archive on DSpace Test:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ dspace community-filiator -r -p 10568/83389 -c 10947/2516
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</span></span><span style="display:flex;"><span>$ dspace community-filiator -s -p 10947/2515 -c 10947/2516
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</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10947/2516
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</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10947/2515
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</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10568/83389
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</span></span><span style="display:flex;"><span>$ dspace index-discovery
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</span></span></code></pre></div><ul>
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<li>I think this is the minimal we can do to avoid a full Discovery reindex which is very expensive</li>
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<li>I helped Maria resize some massive PDFs for upload to CGSpace using GhostScript prepress mode as I had done before in <a href="/cgspace-notes/2023-09/">September, 2023</a>,</li>
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</ul>
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<h2 id="2023-11-08">2023-11-08</h2>
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<ul>
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<li>DSpace 7 Test has very high load again and I see more Java heap space errors in the log</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># grep -c <span style="color:#e6db74">'Caused by: java.lang.OutOfMemoryError: Java heap space'</span> /home/dspace7/log/dspace.log-2023-11-07
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</span></span><span style="display:flex;"><span>35
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</span></span><span style="display:flex;"><span># grep -c <span style="color:#e6db74">'Caused by: java.lang.OutOfMemoryError: Java heap space'</span> /home/dspace7/log/dspace.log
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</span></span><span style="display:flex;"><span>7
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</span></span></code></pre></div><ul>
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<li>I don’t know what is happening… I will increase the heap size from 6144m to 7168m again…</li>
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</ul>
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2023-11/">November, 2023</a></li>
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<li><a href="/cgspace-notes/2023-10/">October, 2023</a></li>
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<li><a href="/cgspace-notes/2023-09/">September, 2023</a></li>
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<li><a href="/cgspace-notes/2023-08/">August, 2023</a></li>
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<li><a href="/cgspace-notes/2023-07/">July, 2023</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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