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Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
I improved the filtering and wrote some Python using pandas to merge my sources more reliably
2023-11-02
Export CGSpace to check missing Initiative collection mappings
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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2023-11-02
Export CGSpace to check missing Initiative collection mappings
Start a harvest on AReS
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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>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
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</header>
<h2 id="2023-11-01">2023-11-01</h2>
<ul>
<li>Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
<ul>
<li>I improved the filtering and wrote some Python using pandas to merge my sources more reliably</li>
</ul>
</li>
</ul>
<h2 id="2023-11-02">2023-11-02</h2>
<ul>
<li>Export CGSpace to check missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<ul>
<li>IFPRI contacted us about importing their Slideshare presentations to CGSpace
<ul>
<li>There are ~1,700 of them and date back to as early as 2008</li>
<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>
</ul>
</li>
</ul>
<h2 id="2023-11-03">2023-11-03</h2>
<ul>
<li>A little bit of work on the CGIAR Climate Change Synthesis</li>
<li>Discuss some CGSpace migration plans with Leigh from IFPRI
<ul>
<li>For their Slideshare content we agreed:
<ul>
<li>Exclude private</li>
<li>Exclude deleted</li>
<li>Exclude non presentation types</li>
<li>Exclude duplicates within the collection for now until we can sort them out</li>
</ul>
</li>
<li>That leaves about 1,500 items out of the 1,700</li>
</ul>
</li>
<li>I did a duplicate check against CGSpace and found 44 items with 1.0 similarity so I removed those</li>
</ul>
<h2 id="2023-11-04">2023-11-04</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>I ran through the list of potential duplicates on the IFPRI Slideshare presentations</li>
</ul>
<h2 id="2023-11-05">2023-11-05</h2>
<ul>
<li>Work with Salem to migrate AReS to the new version</li>
</ul>
<h2 id="2023-11-07">2023-11-07</h2>
<ul>
<li>DSpace 7 Test went down and there is very high load on the server
<ul>
<li>I saw very high load from Java but didn&rsquo;t have time to check exactly what was wrong so I just rebooted the host</li>
<li>A few hours after restarting the system went down again, with very high load from Java again</li>
<li>I see lots of messages like this in the Tomcat log:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>tomcat9[732]: [9955.662s][info ][gc] GC(6291) Pause Full (G1 Compaction Pause) 4085M-&gt;4080M(4096M) 677.251ms
tomcat9[732]: [9955.662s][info ][gc] GC(6290) Concurrent Mark Cycle 677.558ms
tomcat9[732]: [9955.666s][info ][gc] GC(6292) To-space exhausted
</code></pre><ul>
<li>I see some messages in <code>dspace.log</code> about heap space:</li>
</ul>
<pre tabindex="0"><code>Caused by: java.lang.OutOfMemoryError: Java heap space
</code></pre><ul>
<li>I will increase Tomcat&rsquo;s heap from 4096m to 5120m
<ul>
<li>A few hours later it happened again, so I increased the heap from 5120m to 6144m</li>
<li>Not sure what&rsquo;s going on today&hellip;</li>
</ul>
</li>
<li>I tested moving the CGIAR Fund Council community to the CGIAR historic archive on DSpace Test:</li>
</ul>
<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
</span></span><span style="display:flex;"><span>$ dspace community-filiator -s -p 10947/2515 -c 10947/2516
</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10947/2516
</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10947/2515
</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10568/83389
</span></span><span style="display:flex;"><span>$ dspace index-discovery
</span></span></code></pre></div><ul>
<li>I think this is the minimal we can do to avoid a full Discovery reindex which is very expensive</li>
<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>
</ul>
<h2 id="2023-11-08">2023-11-08</h2>
<ul>
<li>DSpace 7 Test has very high load again and I see more Java heap space errors in the log</li>
</ul>
<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">&#39;Caused by: java.lang.OutOfMemoryError: Java heap space&#39;</span> /home/dspace7/log/dspace.log-2023-11-07
</span></span><span style="display:flex;"><span>35
</span></span><span style="display:flex;"><span># grep -c <span style="color:#e6db74">&#39;Caused by: java.lang.OutOfMemoryError: Java heap space&#39;</span> /home/dspace7/log/dspace.log
</span></span><span style="display:flex;"><span>7
</span></span></code></pre></div><ul>
<li>I don&rsquo;t know what is happening&hellip; I will increase the heap size from 6144m to 7168m again&hellip;</li>
<li>I did some work on the value mappings in AReS
<ul>
<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>
<li>Importing duplicates records, so I deleted and re-created the index in Elasticsearch first</li>
<li>Then I started a new harvest on AReS to make sure the mappings are applied</li>
</ul>
</li>
</ul>
<h2 id="2023-11-09">2023-11-09</h2>
<ul>
<li>Ryan asked me for help uploading a large PDF to CGSpace
<ul>
<li>I tried my usual GhostScript preprint invocation and found the size decrease significantly, but some minor artifacts appeared in the images</li>
<li>Interestingly, the <a href="https://ghostscript.com/docs/9.54.0/VectorDevices.htm">GhostScript docs</a> mention that <code>prepress</code> doesn&rsquo;t give the best results:</li>
</ul>
</li>
</ul>
<blockquote>
<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 &lsquo;best&rsquo; quality (where best means closest to the original input) is obtained by not setting this parameter at all (or by using /default).</p>
</blockquote>
<ul>
<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>
</ul>
<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">&#34;&lt;&lt; /ColorACSImageDict &lt;&lt; /VSamples [ 1 1 1 1 ] /HSamples [ 1 1 1 1 ] /QFactor 0.08 /Blend 1 &gt;&gt; /ColorImageDownsampleType /Bicubic /ColorConversionStrategy /LeaveColorUnchanged &gt;&gt; setdistillerparams&#34;</span> -f 137166.pdf
</span></span></code></pre></div><ul>
<li>This looks much better, and is still much smaller than the original
<ul>
<li>Also, I used <code>pdfimages</code> to extract all the images from the original and the one above and found:</li>
</ul>
</li>
</ul>
<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-*
</span></span><span style="display:flex;"><span>886M images-default-dct
</span></span><span style="display:flex;"><span>1012M images-original
</span></span></code></pre></div><ul>
<li>And from <a href="https://www.wecompress.com/en/analyze">WeCompress&rsquo;s analysis</a> I see that the images are 85% of the size of the PDF</li>
</ul>
<h2 id="2023-11-10">2023-11-10</h2>
<ul>
<li>I finished checking the IFPRI Slideshare records and added some tagging of countries, regions, and CRPs and then uploaded them to CGSpace</li>
</ul>
<h2 id="2023-11-11">2023-11-11</h2>
<ul>
<li>Salem fixed a bug on OpenRXV that was splitting country values by &ldquo;,&rdquo; before matching them with ISO countries</li>
<li>I exported CGSpace to check for missing Initiative collection mappings</li>
<li>Start a fresh harvest on AReS</li>
</ul>
<h2 id="2023-11-16">2023-11-16</h2>
<ul>
<li>Discuss mapping ICARDA outputs from Initiatives to ICARDA collections on CGSpace
<ul>
<li>I added MEL&rsquo;s CGSpace user to the administrator group of a handful of collections</li>
<li>I also did a batch mapping of 274 existing Initiative outputs from ICARDA to the relevant collections</li>
</ul>
</li>
</ul>
<h2 id="2023-11-18">2023-11-18</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-11-22">2023-11-22</h2>
<ul>
<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>:
<ul>
<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>
<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>
</ul>
</li>
<li>And the numbers match those in my dspace-statisitcs-api <em>exactly</em>!</li>
<li>This can be useful to get an individual DSpace object&rsquo;s stats, but there is no way to iterate over all objects like all items&hellip;
<ul>
<li>We can look at using this to draw stats on the community, collection, and item pages</li>
</ul>
</li>
</ul>
<h2 id="2023-11-23">2023-11-23</h2>
<ul>
<li>Brian King was asking me how many PDFs we had in CGSpace so I got a rough estimate using this SQL query:</li>
</ul>
<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=&#39;application/pdf&#39;);
</span></span><span style="display:flex;"><span> count
</span></span><span style="display:flex;"><span>───────
</span></span><span style="display:flex;"><span> 47818
</span></span><span style="display:flex;"><span>(1 row)
</span></span></code></pre></div><ul>
<li>It&rsquo;s been some time since I looked at our Solr statistics to find new bots
<ul>
<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:
<ul>
<li>GuzzleHttp/7</li>
<li><a href="mailto:Owler@ows.eu">Owler@ows.eu</a>/1</li>
<li>newspaperjs</li>
</ul>
</li>
</ul>
</li>
<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>
</ul>
<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
</span></span><span style="display:flex;"><span>Purging 30 hits from ubermetrics in statistics
</span></span><span style="display:flex;"><span>Purging 59 hits from curb in statistics
</span></span><span style="display:flex;"><span>Purging 36 hits from bitdiscovery in statistics
</span></span><span style="display:flex;"><span>Purging 87 hits from omgili in statistics
</span></span><span style="display:flex;"><span>Purging 47 hits from Vizzit in statistics
</span></span><span style="display:flex;"><span>Purging 109 hits from Java\/17-ea in statistics
</span></span><span style="display:flex;"><span>Purging 40 hits from AdobeUxTechC4-Async in statistics
</span></span><span style="display:flex;"><span>Purging 21 hits from ZaloPC-win32-24v473 in statistics
</span></span><span style="display:flex;"><span>Purging 21 hits from nbertaupete95 in statistics
</span></span><span style="display:flex;"><span>Purging 52 hits from Scoop\.it in statistics
</span></span><span style="display:flex;"><span>Purging 16 hits from WebAPIClient in statistics
</span></span><span style="display:flex;"><span>Purging 241 hits from RStudio in statistics
</span></span><span style="display:flex;"><span>Purging 1255 hits from ^MEL in statistics
</span></span><span style="display:flex;"><span>Purging 47850 hits from GuzzleHttp in statistics
</span></span><span style="display:flex;"><span>Purging 8714 hits from Owler in statistics
</span></span><span style="display:flex;"><span>Purging 1083 hits from newspaperjs in statistics
</span></span><span style="display:flex;"><span>Purging 369 hits from ^Chrome$ in statistics
</span></span><span style="display:flex;"><span>Purging 1474 hits from curl in statistics
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 61504
</span></span></code></pre></div><ul>
<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:
<ul>
<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>
<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>
</ul>
</li>
<li>I&rsquo;m gonna add those to our overrides and purge them:</li>
</ul>
<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
</span></span><span style="display:flex;"><span>Purging 35816 hits from ^mozilla in statistics
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 35816
</span></span></code></pre></div><h2 id="2023-11-30">2023-11-30</h2>
<ul>
<li>Minor updates to our OAI MODS crosswalk
<ul>
<li>Stefano found a minor markup issue with our alternative titles (<code>&lt;titleInfo&gt;</code> tag)</li>
</ul>
</li>
<li>Very high load on CGSpace since after lunch
<ul>
<li>I killed some locks that had been stuck for a few hours</li>
</ul>
</li>
</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2024-11/">November, 2024</a></li>
<li><a href="/cgspace-notes/2024-10/">October, 2024</a></li>
<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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