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Work on CGSpace duplicate DOIs more
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<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/2024-04/">April, 2024</a></h2>
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<time datetime="2024-04-04T10:23:00+03:00">Thu Apr 04, 2024</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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<h2 id="2024-04-04">2024-04-04</h2>
<ul>
<li>Work on CGSpace duplicate DOIs more</li>
</ul>
<h2 id="2024-04-08">2024-04-08</h2>
<ul>
<li>Start working on IFPRI&rsquo;s 2022 batch import
<ul>
<li>I ran the duplicate checker against CGSpace and started downloading all linked PDFs</li>
</ul>
</li>
</ul>
<h2 id="2024-04-09">2024-04-09</h2>
<ul>
<li>Continue working on IFPRI&rsquo;s 2022 batch import
<ul>
<li>I started validating the potential duplicates in OpenRefine</li>
</ul>
</li>
</ul>
<h2 id="2024-04-12">2024-04-12</h2>
<ul>
<li>Finish working on the 650 IFPRI 2022 records that were not already on CGSpace, then uploaded them
<ul>
<li>I need to merge the metadata for the remaining 212 that are already on CGSpace</li>
</ul>
</li>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
</ul>
<h2 id="2024-04-13">2024-04-13</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
</ul>
<h2 id="2024-04-14">2024-04-14</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
</ul>
<h2 id="2024-04-15">2024-04-15</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
<li>Delete ~260 duplicate metadata values using the elaborate SQL and sort method I documented here: <a href="https://github.com/DSpace/DSpace/issues/8253#issuecomment-1331756418">https://github.com/DSpace/DSpace/issues/8253#issuecomment-1331756418</a></li>
<li>Tony noticed that the DSpace 7 REST API is very slow with the embeds so I profiled a bit:</li>
</ul>
<pre tabindex="0"><code>$ time curl -s -o /dev/null &#39;https://cgspace.cgiar.org/server/api/discover/search/objects?query=cg.identifier.project%3AIFPRI*&amp;scope=8f1e9650-fe87-4e6e-889a-1cacfb747408&amp;page=0&amp;size=100&amp;embed=thumbnail,bundles/bitstreams&amp;sort=dcterms.issued,desc&#39;
curl -s -o /dev/null 0.01s user 0.01s system 0% cpu 47.515 total
$ time curl -s -o /dev/null &#39;https://cgspace.cgiar.org/server/api/discover/search/objects?query=cg.identifier.project%3AIFPRI*&amp;scope=8f1e9650-fe87-4e6e-889a-1cacfb747408&amp;page=0&amp;size=100&amp;sort=dcterms.issued,desc&#39;
curl -s -o /dev/null 0.01s user 0.01s system 0% cpu 4.764 total
</code></pre><ul>
<li>Finalize processing the remaining 206 items from the IFPRI 2022 batch set that already existed on CGSpace
<ul>
<li>I merged metadata with the existing items</li>
<li>There are still six remaining items that I identified as being duplicates (3x2) in the IFPRI set itself</li>
</ul>
</li>
</ul>
<h2 id="2024-04-16">2024-04-16</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
<li>Assist Deborah with an advanced query on CGSpace for biodiversity and health:</li>
</ul>
<pre tabindex="0"><code>dcterms.issued:[2010 TO 2024] AND dcterms.type:&#34;Journal Article&#34; AND (dc.title:&#34;biodiversity&#34; OR dcterms.subject:&#34;biodiversity&#34; OR dc.title:&#34;health&#34; OR dcterms.subject:&#34;health&#34;)
</code></pre><ul>
<li>Remove CIMMYT URLs and citations from 277 journal articles on CGSpace since it is a bit tacky
<ul>
<li>I used this Jython expression in OpenRefine with <a href="https://citation.crosscite.org/docs.html">Crossref&rsquo;s content negotiation</a> to get citations for all DOIs:</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> urllib2
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span>doi <span style="color:#f92672">=</span> cells[<span style="color:#e6db74">&#39;cg.identifier.doi[en_US]&#39;</span>]<span style="color:#f92672">.</span>value
</span></span><span style="display:flex;"><span>url <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;https://api.crossref.org/works/&#34;</span> <span style="color:#f92672">+</span> doi <span style="color:#f92672">+</span> <span style="color:#e6db74">&#34;/transform/text/x-bibliography&#34;</span>
</span></span><span style="display:flex;"><span>useragent <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;Python (mailto:a.o@cgiar.org)&#34;</span>
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span>request <span style="color:#f92672">=</span> urllib2<span style="color:#f92672">.</span>Request(url<span style="color:#f92672">.</span>encode(<span style="color:#e6db74">&#34;utf-8&#34;</span>), headers<span style="color:#f92672">=</span>{<span style="color:#e6db74">&#34;User-Agent&#34;</span> : useragent})
</span></span><span style="display:flex;"><span>get <span style="color:#f92672">=</span> urllib2<span style="color:#f92672">.</span>urlopen(request)
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> get<span style="color:#f92672">.</span>read()<span style="color:#f92672">.</span>decode(<span style="color:#e6db74">&#39;utf-8&#39;</span>)
</span></span></code></pre></div><ul>
<li>It took ten or so minutes for it to finish (and note this is Python 2 inside OpenRefine so I had to be careful with Unicode), but worked well!</li>
</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</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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