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I learned how to use the Levenshtein functions in PostgreSQL
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The thing is that there is a limit of 255 characters for these functions in PostgreSQL so you need to truncate the strings before comparing
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Also, the trgm functions I’ve used before are case insensitive, but Levenshtein is not, so you need to make sure to lower case both strings first
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<meta name="twitter:description" content="2022-07-02
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I learned how to use the Levenshtein functions in PostgreSQL
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The thing is that there is a limit of 255 characters for these functions in PostgreSQL so you need to truncate the strings before comparing
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Also, the trgm functions I’ve used before are case insensitive, but Levenshtein is not, so you need to make sure to lower case both strings first
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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/2022-07/">July, 2022</a></h2>
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<time datetime="2022-07-02T14:07:36+03:00">Sat Jul 02, 2022</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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</header>
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<h2 id="2022-07-02">2022-07-02</h2>
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<ul>
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<li>I learned how to use the Levenshtein functions in PostgreSQL
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<ul>
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<li>The thing is that there is a limit of 255 characters for these functions in PostgreSQL so you need to truncate the strings before comparing</li>
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<li>Also, the trgm functions I’ve used before are case insensitive, but Levenshtein is not, so you need to make sure to lower case both strings first</li>
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</ul>
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</li>
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</ul>
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<ul>
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<li>A working query checking for duplicates in the recent AfricaRice items is:</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/dspace= ☘ SELECT text_value FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND levenshtein_less_equal(LOWER('International Trade and Exotic Pests: The Risks for Biodiversity and African Economies'), LEFT(LOWER(text_value), 255), 3) <= 3;
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</span></span><span style="display:flex;"><span> text_value
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</span></span><span style="display:flex;"><span>────────────────────────────────────────────────────────────────────────────────────────
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</span></span><span style="display:flex;"><span> International trade and exotic pests: the risks for biodiversity and African economies
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</span></span><span style="display:flex;"><span>(1 row)
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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>Time: 399.751 ms
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</span></span></code></pre></div><ul>
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<li>There is a great <a href="https://www.crunchydata.com/blog/fuzzy-name-matching-in-postgresql">blog post discussing Soundex with Levenshtein</a> and creating indexes to make them faster</li>
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<li>I want to do some proper checks of accuracy and speed against my trigram method</li>
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</ul>
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<h2 id="2022-07-03">2022-07-03</h2>
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<ul>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2022-07-04">2022-07-04</h2>
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<ul>
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<li>Linode told me that CGSpace had high load yesterday
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<ul>
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<li>I also got some up and down notices from UptimeRobot</li>
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<li>Looking now, I see there was a very high CPU and database pool load, but a mostly normal DSpace session count</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2022/07/cpu-day.png" alt="CPU load day">
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<img src="/cgspace-notes/2022/07/jmx_tomcat_dbpools-day.png" alt="JDBC pool day"></p>
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<ul>
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<li>Seems we have some old database transactions since 2022-06-27:</li>
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</ul>
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<p><img src="/cgspace-notes/2022/07/postgres_locks_ALL-week.png" alt="PostgreSQL locks week">
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<img src="/cgspace-notes/2022/07/postgres_querylength_ALL-week.png" alt="PostgreSQL query length week"></p>
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<ul>
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<li>Looking at the top connections to nginx yesterday:</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># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.1 | sort | uniq -c | sort -h | tail
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</span></span><span style="display:flex;"><span> 1132 64.124.8.34
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</span></span><span style="display:flex;"><span> 1146 2a01:4f8:1c17:5550::1
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</span></span><span style="display:flex;"><span> 1380 137.184.159.211
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</span></span><span style="display:flex;"><span> 1533 64.124.8.59
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</span></span><span style="display:flex;"><span> 4013 80.248.237.167
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</span></span><span style="display:flex;"><span> 4776 54.195.118.125
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</span></span><span style="display:flex;"><span> 10482 45.5.186.2
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</span></span><span style="display:flex;"><span> 11177 172.104.229.92
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</span></span><span style="display:flex;"><span> 15855 2a01:7e00::f03c:91ff:fe9a:3a37
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</span></span><span style="display:flex;"><span> 22179 64.39.98.251
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</span></span></code></pre></div><ul>
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<li>And the total number of unique IPs:</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># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.1 | sort -u | wc -l
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</span></span><span style="display:flex;"><span>6952
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</span></span></code></pre></div><ul>
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<li>This seems low, so it must have been from the request patterns by certain visitors
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<ul>
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<li>64.39.98.251 is Qualys, and I’m debating blocking <a href="https://pci.qualys.com/static/help/merchant/getting_started/check_scanner_ip_addresses.htm">all their IPs</a> using a geo block in nginx (need to test)</li>
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<li>The top few are known ILRI and other CGIAR scrapers, but 80.248.237.167 is on InternetVikings in Sweden, using a normal user agentand scraping Discover</li>
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<li>64.124.8.59 is making requests with a normal user agent and belongs to Castle Global or Zayo</li>
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</ul>
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</li>
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<li>I ran all system updates and rebooted the server (could have just restarted PostgreSQL but I thought I might as well do everything)</li>
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<li>I implemented a geo mapping for the user agent mapping AND the nginx <code>limit_req_zone</code> by extracting the networks into an external file and including it in two different geo mapping blocks
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<ul>
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<li>This is clever and relies on the fact that we can use defaults in both cases</li>
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<li>First, we map the user agent of requests from these networks to “bot” so that Tomcat and Solr handle them accordingly</li>
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<li>Second, we use this as a key in a <code>limit_req_zone</code>, which relies on a default mapping of ’’ (and nginx doesn’t evaluate empty cache keys)</li>
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</ul>
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</li>
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<li>I noticed that CIP uploaded a number of Georgian presentations with <code>dcterms.language</code> set to English and Other so I changed them to “ka”
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<ul>
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<li>Perhaps we need to update our list of languages to include all instead of the most common ones</li>
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</ul>
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</li>
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<li>I wrote a script <code>ilri/iso-639-value-pairs.py</code> to extract the names and Alpha 2 codes for all ISO 639-1 languages from pycountry and added them to <code>input-forms.xml</code></li>
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</ul>
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<h2 id="2022-07-06">2022-07-06</h2>
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<ul>
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<li>CGSpace went down and up a few times due to high load
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<ul>
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<li>I found one host in Romania making very high speed requests with a normal user agent (<code>Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.2; WOW64; Trident/7.0; .NET4.0E; .NET4.0C</code>):</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># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log | sort | uniq -c | sort -h | tail -n <span style="color:#ae81ff">10</span>
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</span></span><span style="display:flex;"><span> 516 142.132.248.90
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</span></span><span style="display:flex;"><span> 525 157.55.39.234
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</span></span><span style="display:flex;"><span> 587 66.249.66.21
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</span></span><span style="display:flex;"><span> 593 95.108.213.59
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</span></span><span style="display:flex;"><span> 1372 137.184.159.211
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</span></span><span style="display:flex;"><span> 4776 54.195.118.125
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</span></span><span style="display:flex;"><span> 5441 205.186.128.185
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</span></span><span style="display:flex;"><span> 6267 45.5.186.2
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</span></span><span style="display:flex;"><span> 15839 2a01:7e00::f03c:91ff:fe9a:3a37
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</span></span><span style="display:flex;"><span> 36114 146.19.75.141
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</span></span></code></pre></div><ul>
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<li>I added 146.19.75.141 to the list of bot networks in nginx</li>
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<li>While looking at the logs I started thinking about Bing again
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<ul>
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<li>They apparently <a href="https://www.bing.com/toolbox/bingbot.json">publish a list of all their networks</a></li>
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<li>I wrote a script to use <code>prips</code> to <a href="https://stackoverflow.com/a/52501093/1996540">print the IPs for each network</a></li>
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<li>The script is <code>bing-networks-to-ips.sh</code></li>
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<li>From Bing’s IPs alone I purged 145,403 hits… sheesh</li>
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</ul>
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</li>
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<li>Delete two items on CGSpace for Margarita because she was getting the “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:0b26875a-…” error
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<ul>
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<li>This is the same DSpace 6 bug I noticed in 2021-03, 2021-04, and 2021-05</li>
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</ul>
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</li>
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<li>Update some <code>cg.audience</code> metadata to use “Academics” instead of “Academicians”:</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=# UPDATE metadatavalue SET text_value='Academics' WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=144 AND text_value='Academicians';
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</span></span><span style="display:flex;"><span>UPDATE 104
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</span></span></code></pre></div><ul>
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<li>I will also have to remove “Academicians” from input-forms.xml</li>
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</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2022-07/">July, 2022</a></li>
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<li><a href="/cgspace-notes/2022-06/">June, 2022</a></li>
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<li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
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<li><a href="/cgspace-notes/2022-04/">April, 2022</a></li>
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<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
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<h4>Links</h4>
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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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