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Last week Bizu reported an issue with the “browse by issue date” drop down
I verified it, and suspect it could be due to missing issue dates…
It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
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Last week Bizu reported an issue with the “browse by issue date” drop down
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It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
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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/2024-03/">March, 2024</a></h2>
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<time datetime="2024-03-01T09:55:00+03:00">Fri Mar 01, 2024</time>
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<h2 id="2024-03-01">2024-03-01</h2>
<ul>
<li>Last week Bizu reported an issue with the “browse by issue date” drop down
<ul>
<li>I verified it, and suspect it could be due to missing issue dates…</li>
<li>It might be this issue: <a href="https://github.com/DSpace/dspace-angular/issues/2808">https://github.com/DSpace/dspace-angular/issues/2808</a></li>
</ul>
</li>
</ul>
<ul>
<li>I spent some time trying to reproduce the bug affecting <code>onebox</code> fields that are configured to use external vocabularies and are not repeatable
<ul>
<li>I filed an issue: <a href="https://github.com/DSpace/dspace-angular/issues/2846">https://github.com/DSpace/dspace-angular/issues/2846</a></li>
</ul>
</li>
</ul>
<h2 id="2024-03-03">2024-03-03</h2>
<ul>
<li>I did some cleanups on abstracts, licenses, and dates from CrossRef</li>
<li>I also did some minor cleanups to affiliations because I saw some incorrect and duplicate ones in our list</li>
</ul>
<h2 id="2024-03-05">2024-03-05</h2>
<ul>
<li>I tried a new technique to get some affiliations from Crossref using OpenRefine
<ul>
<li>First I split them and clustered, resolving a few hundred clusters out of 1500 (!)</li>
<li>Then I used a custom text facet with a few dozen CGIAR and other large affiliations to reduce the work</li>
<li>Then I joined them with our affiliations, paying no attention to duplicates</li>
<li>Then I deduped them using the Jython technique I learned in 2023-02</li>
</ul>
</li>
</ul>
<h2 id="2024-03-06">2024-03-06</h2>
<ul>
<li>Peter sent me some more corrections for the authors that I had sent him in 2023-12</li>
</ul>
<h2 id="2024-03-08">2024-03-08</h2>
<ul>
<li>IFPRI sent me their 2023 records from CONTENTdm so I started working on those
<ul>
<li>I found a way to match their ORCID identifiers in our list using Jython in OpenRefine:</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> re
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">with</span> open(<span style="color:#e6db74">r</span><span style="color:#e6db74">"/tmp/cg-creator-identifier.txt"</span>,<span style="color:#e6db74">'r'</span>) <span style="color:#66d9ef">as</span> f :
</span></span><span style="display:flex;"><span> orcid_ids <span style="color:#f92672">=</span> [orcid_id<span style="color:#f92672">.</span>strip() <span style="color:#66d9ef">for</span> orcid_id <span style="color:#f92672">in</span> f]
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span>matched <span style="color:#f92672">=</span> <span style="color:#66d9ef">False</span>
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">for</span> orcid_id <span style="color:#f92672">in</span> orcid_ids:
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">if</span> re<span style="color:#f92672">.</span>search(<span style="color:#e6db74">r</span><span style="color:#e6db74">'.+: </span><span style="color:#e6db74">{}</span><span style="color:#e6db74">'</span><span style="color:#f92672">.</span>format(value), orcid_id):
</span></span><span style="display:flex;"><span> matched <span style="color:#f92672">=</span> <span style="color:#66d9ef">True</span>
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">break</span>
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">if</span> matched:
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">return</span> orcid_id
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">else</span>:
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">return</span> value
</span></span></code></pre></div><ul>
<li>I realized that <a href="https://www.unicef.org/about-unicef/frequently-asked-questions#3">UNICEF was renamed to its current name in 1953</a> so I replaced all other variations in our vocabularies and metadata:</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">UPDATE</span> metadatavalue <span style="color:#66d9ef">SET</span> text_value<span style="color:#f92672">=</span><span style="color:#e6db74">'United Nations Children''s Fund'</span> <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item) <span style="color:#66d9ef">AND</span> text_value <span style="color:#66d9ef">IN</span> (<span style="color:#e6db74">'United Nations International Children''s Emergency Fund'</span>, <span style="color:#e6db74">'United Nations International Children''s Emergency Fund'</span>, <span style="color:#e6db74">'UNICEF'</span>);
</span></span></code></pre></div><ul>
<li>Note the use of two single quotes to escape the one in the name</li>
</ul>
<h2 id="2024-03-11">2024-03-11</h2>
<ul>
<li>Experimenting with moving some of my Python scripts to the DSpace 7 REST API
<ul>
<li>I need a way to get UUIDs for Handles…</li>
<li>Seems that I can use a Discovery query like: <a href="https://dspace7test.ilri.org/server/api/discover/search/objects?dsoType=item&query=handle:10568/130864">https://dspace7test.ilri.org/server/api/discover/search/objects?dsoType=item&query=handle:10568/130864</a></li>
<li>Then just take the first result…?</li>
</ul>
</li>
<li>I spent some time working on the script get abstracts from CGSpace, and found a bug in my logic
<ul>
<li>I also noticed that one item had two abstracts, but the first one was blank!</li>
<li>Looking deeper, I found 113 blank metadata values so I deleted those:</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>;
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">DELETE</span> <span style="color:#66d9ef">FROM</span> metadatavalue <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item) <span style="color:#66d9ef">AND</span> text_value<span style="color:#f92672">=</span><span style="color:#e6db74">''</span>;
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">COMMIT</span>;
</span></span></code></pre></div><ul>
<li>I also found a few dozen items with “N/A” for their citation, so I deleted those too:</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>;
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">DELETE</span> <span style="color:#66d9ef">FROM</span> metadatavalue <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item) <span style="color:#66d9ef">AND</span> text_value<span style="color:#f92672">=</span><span style="color:#e6db74">'N/A'</span> <span style="color:#66d9ef">AND</span> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">146</span>;
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">COMMIT</span>;
</span></span></code></pre></div><ul>
<li>I deployed the change to disable Angular SSR’s <code>inlineCriticalCss</code> on production because we had heavy load on the frontend and I’ve been meaning to do this permanently for some time</li>
<li>Maria asked me for a CSV with all the broken Bioversity permalinks so I exported them for her:</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>$ csvcut -c <span style="color:#e6db74">'id,dc.title[en_US],dc.identifier.uri[en_US],cg.link.permalink[en_US]'</span> ~/Downloads/2024-03-05-cgspace.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvgrep -c 'cg.link.permalink[en_US]' -r '^.+$' > /tmp/2024-03-11-Bioversity-Permalinks.csv
</span></span></code></pre></div><!-- raw HTML omitted -->
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<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>
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