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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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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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<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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<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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<li>I did some work on the value mappings in AReS
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<ul>
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<li>I wanted to test the import/export feature, and found that I could get a JSON and convert it to CSV for manipulation in OpenRefine</li>
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<li>Importing duplicates records, so I deleted and re-created the index in Elasticsearch first</li>
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<li>Then I started a new harvest on AReS to make sure the mappings are applied</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-11-09">2023-11-09</h2>
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<ul>
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<li>Ryan asked me for help uploading a large PDF to CGSpace
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<ul>
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<li>I tried my usual GhostScript preprint invocation and found the size decrease significantly, but some minor artifacts appeared in the images</li>
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<li>Interestingly, the <a href="https://ghostscript.com/docs/9.54.0/VectorDevices.htm">GhostScript docs</a> mention that <code>prepress</code> doesn’t give the best results:</li>
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</ul>
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</li>
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</ul>
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<blockquote>
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<p>Please be aware that the /prepress setting does not indicate the highest quality conversion. Using any of these presets will involve altering the input, and as such may result in a PDF of poorer quality (compared to the input) than simply using the defaults. The ‘best’ quality (where best means closest to the original input) is obtained by not setting this parameter at all (or by using /default).</p>
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</blockquote>
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<ul>
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<li>Also, I found <a href="https://stackoverflow.com/questions/40849325/ghostscript-pdfwrite-specify-jpeg-quality">a question on StackOverflow discussing some further techniques for PDFs with images</a>:</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>$ gs -sOutputFile<span style="color:#f92672">=</span>137166-default-dct.pdf -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dNOPAUSE -dBATCH -dPDFSETTINGS<span style="color:#f92672">=</span>/default -c <span style="color:#e6db74">"<< /ColorACSImageDict << /VSamples [ 1 1 1 1 ] /HSamples [ 1 1 1 1 ] /QFactor 0.08 /Blend 1 >> /ColorImageDownsampleType /Bicubic /ColorConversionStrategy /LeaveColorUnchanged >> setdistillerparams"</span> -f 137166.pdf
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</span></span></code></pre></div><ul>
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<li>This looks much better, and is still much smaller than the original
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<ul>
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<li>Also, I used <code>pdfimages</code> to extract all the images from the original and the one above and found:</li>
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</ul>
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</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>$ du -sh images-*
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</span></span><span style="display:flex;"><span>886M images-default-dct
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</span></span><span style="display:flex;"><span>1012M images-original
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</span></span></code></pre></div><ul>
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<li>And from <a href="https://www.wecompress.com/en/analyze">WeCompress’s analysis</a> I see that the images are 85% of the size of the PDF</li>
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</ul>
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<h2 id="2023-11-10">2023-11-10</h2>
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<ul>
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<li>I finished checking the IFPRI Slideshare records and added some tagging of countries, regions, and CRPs and then uploaded them to CGSpace</li>
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</ul>
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<h2 id="2023-11-11">2023-11-11</h2>
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<ul>
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<li>Salem fixed a bug on OpenRXV that was splitting country values by “,” before matching them with ISO countries</li>
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<li>I exported CGSpace to check for missing Initiative collection mappings</li>
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<li>Start a fresh harvest on AReS</li>
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</ul>
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<h2 id="2023-11-16">2023-11-16</h2>
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<ul>
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<li>Discuss mapping ICARDA outputs from Initiatives to ICARDA collections on CGSpace
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<ul>
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<li>I added MEL’s CGSpace user to the administrator group of a handful of collections</li>
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<li>I also did a batch mapping of 274 existing Initiative outputs from ICARDA to the relevant collections</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-11-18">2023-11-18</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>Start a harvest on AReS</li>
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</ul>
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<h2 id="2023-11-22">2023-11-22</h2>
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<ul>
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<li>I was checking out the <a href="https://github.com/DSpace/RestContract/blob/main/statistics-reports.md">DSpace 7 statistics</a> again and found that we have total visits and total downloads for each DSpace object, for example <a href="https://dspace7test.ilri.org/items/3f1b9605-f5ff-4bbb-8c89-d6fe4157f748">this item</a>:
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<ul>
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<li>TotalVisits: <a href="https://dspace7test.ilri.org/server/api/statistics/usagereports/3f1b9605-f5ff-4bbb-8c89-d6fe4157f748_TotalVisits">https://dspace7test.ilri.org/server/api/statistics/usagereports/3f1b9605-f5ff-4bbb-8c89-d6fe4157f748_TotalVisits</a></li>
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<li>TotalDownloads: <a href="https://dspace7test.ilri.org/server/api/statistics/usagereports/3f1b9605-f5ff-4bbb-8c89-d6fe4157f748_TotalDownloads">https://dspace7test.ilri.org/server/api/statistics/usagereports/3f1b9605-f5ff-4bbb-8c89-d6fe4157f748_TotalDownloads</a></li>
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</ul>
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</li>
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<li>And the numbers match those in my dspace-statisitcs-api <em>exactly</em>!</li>
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<li>This can be useful to get an individual DSpace object’s stats, but there is no way to iterate over all objects like all items…
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<ul>
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<li>We can look at using this to draw stats on the community, collection, and item pages</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-11-23">2023-11-23</h2>
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<ul>
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<li>Brian King was asking me how many PDFs we had in CGSpace so I got a rough estimate using this SQL query:</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>localhost/dspace7= ☘ SELECT COUNT(uuid) FROM bitstream WHERE bitstream_format_id=(SELECT bitstream_format_id FROM bitstreamformatregistry WHERE mimetype='application/pdf');
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</span></span><span style="display:flex;"><span> count
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</span></span><span style="display:flex;"><span>───────
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</span></span><span style="display:flex;"><span> 47818
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</span></span><span style="display:flex;"><span>(1 row)
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</span></span></code></pre></div><ul>
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<li>It’s been some time since I looked at our Solr statistics to find new bots
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<ul>
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<li>I found a few new ones that I <a href="https://github.com/atmire/COUNTER-Robots/pull/60">submitted to COUNTER-Robots</a> and added to our local bot list:
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<ul>
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<li>GuzzleHttp/7</li>
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<li><a href="mailto:Owler@ows.eu">Owler@ows.eu</a>/1</li>
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<li>newspaperjs</li>
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</ul>
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</li>
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</ul>
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</li>
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<li>I ran my old <code>check-spider-hits.sh</code> script with a list of bots from our local overrides to purge hits from Solr:</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>$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p
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</span></span><span style="display:flex;"><span>Purging 30 hits from ubermetrics in statistics
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</span></span><span style="display:flex;"><span>Purging 59 hits from curb in statistics
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</span></span><span style="display:flex;"><span>Purging 36 hits from bitdiscovery in statistics
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</span></span><span style="display:flex;"><span>Purging 87 hits from omgili in statistics
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</span></span><span style="display:flex;"><span>Purging 47 hits from Vizzit in statistics
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</span></span><span style="display:flex;"><span>Purging 109 hits from Java\/17-ea in statistics
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</span></span><span style="display:flex;"><span>Purging 40 hits from AdobeUxTechC4-Async in statistics
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</span></span><span style="display:flex;"><span>Purging 21 hits from ZaloPC-win32-24v473 in statistics
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</span></span><span style="display:flex;"><span>Purging 21 hits from nbertaupete95 in statistics
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</span></span><span style="display:flex;"><span>Purging 52 hits from Scoop\.it in statistics
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</span></span><span style="display:flex;"><span>Purging 16 hits from WebAPIClient in statistics
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</span></span><span style="display:flex;"><span>Purging 241 hits from RStudio in statistics
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</span></span><span style="display:flex;"><span>Purging 1255 hits from ^MEL in statistics
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</span></span><span style="display:flex;"><span>Purging 47850 hits from GuzzleHttp in statistics
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</span></span><span style="display:flex;"><span>Purging 8714 hits from Owler in statistics
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</span></span><span style="display:flex;"><span>Purging 1083 hits from newspaperjs in statistics
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</span></span><span style="display:flex;"><span>Purging 369 hits from ^Chrome$ in statistics
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</span></span><span style="display:flex;"><span>Purging 1474 hits from curl in statistics
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 61504
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</span></span></code></pre></div><ul>
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<li>I also noticed 35,000 requests over the past few years from lowercase user agents, which is <a href="https://developers.whatismybrowser.com/api/features/user-agent-checks/weird/#all_lower_case">definitely weird</a>, for example:
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<ul>
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<li><code>mozilla/5.0 (windows nt 10.0; win64; x64) applewebkit/537.36 (khtml, like gecko) chrome/89.0.4389.90 safari/537.36</code></li>
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<li><code>mozilla/5.0 (windows nt 10.0; win64; x64) applewebkit/537.36 (khtml, like gecko) chrome/90.0.4430.93 safari/537.36</code></li>
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</ul>
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</li>
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<li>I’m gonna add those to our overrides and purge them:</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>$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p
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</span></span><span style="display:flex;"><span>Purging 35816 hits from ^mozilla in statistics
|
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
|
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 35816
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</span></span></code></pre></div><h2 id="2023-11-30">2023-11-30</h2>
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<ul>
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<li>Minor updates to our OAI MODS crosswalk
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<ul>
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<li>Stefano found a minor markup issue with our alternative titles (<code><titleInfo></code> tag)</li>
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</ul>
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</li>
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<li>Very high load on CGSpace since after lunch
|
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<ul>
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<li>I killed some locks that had been stuck for a few hours</li>
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</ul>
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</li>
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</ul>
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