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<meta property="og:description" content="2024-03-01
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Last week Bizu reported an issue with the “browse by issue date” drop down
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I verified it, and suspect it could be due to missing issue dates…
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It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
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<meta name="twitter:title" content="March, 2024"/>
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<meta name="twitter:description" content="2024-03-01
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Last week Bizu reported an issue with the “browse by issue date” drop down
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I verified it, and suspect it could be due to missing issue dates…
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It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
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"/>
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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/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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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="2024-03-01">2024-03-01</h2>
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<ul>
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<li>Last week Bizu reported an issue with the “browse by issue date” drop down
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<ul>
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<li>I verified it, and suspect it could be due to missing issue dates…</li>
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<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>
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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>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
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<ul>
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<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>
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</ul>
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</li>
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</ul>
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<h2 id="2024-03-03">2024-03-03</h2>
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<ul>
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<li>I did some cleanups on abstracts, licenses, and dates from CrossRef</li>
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<li>I also did some minor cleanups to affiliations because I saw some incorrect and duplicate ones in our list</li>
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</ul>
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<h2 id="2024-03-05">2024-03-05</h2>
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<ul>
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<li>I tried a new technique to get some affiliations from Crossref using OpenRefine
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<ul>
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<li>First I split them and clustered, resolving a few hundred clusters out of 1500 (!)</li>
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<li>Then I used a custom text facet with a few dozen CGIAR and other large affiliations to reduce the work</li>
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<li>Then I joined them with our affiliations, paying no attention to duplicates</li>
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<li>Then I deduped them using the Jython technique I learned in 2023-02</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-03-06">2024-03-06</h2>
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<ul>
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<li>Peter sent me some more corrections for the authors that I had sent him in 2023-12</li>
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</ul>
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<h2 id="2024-03-08">2024-03-08</h2>
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<ul>
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<li>IFPRI sent me their 2023 records from CONTENTdm so I started working on those
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<ul>
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<li>I found a way to match their ORCID identifiers in our list using Jython in OpenRefine:</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> re
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</span></span><span style="display:flex;"><span>
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</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 :
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</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]
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span>matched <span style="color:#f92672">=</span> <span style="color:#66d9ef">False</span>
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">for</span> orcid_id <span style="color:#f92672">in</span> orcid_ids:
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</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):
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</span></span><span style="display:flex;"><span> matched <span style="color:#f92672">=</span> <span style="color:#66d9ef">True</span>
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</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">break</span>
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">if</span> matched:
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</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">return</span> orcid_id
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">else</span>:
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</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">return</span> value
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</span></span></code></pre></div><ul>
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<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>
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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-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>);
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</span></span></code></pre></div><ul>
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<li>Note the use of two single quotes to escape the one in the name</li>
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</ul>
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<h2 id="2024-03-11">2024-03-11</h2>
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<ul>
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<li>Experimenting with moving some of my Python scripts to the DSpace 7 REST API
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<ul>
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<li>I need a way to get UUIDs for Handles…</li>
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<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>
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<li>Then just take the first result…?</li>
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</ul>
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</li>
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<li>I spent some time working on the script get abstracts from CGSpace, and found a bug in my logic
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<ul>
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<li>I also noticed that one item had two abstracts, but the first one was blank!</li>
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<li>Looking deeper, I found 113 blank metadata values so I deleted those:</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>;
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</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>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">COMMIT</span>;
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</span></span></code></pre></div><ul>
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<li>I also found a few dozen items with “N/A” for their citation, so I deleted those too:</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>;
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</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>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">COMMIT</span>;
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</span></span></code></pre></div><!-- raw HTML omitted -->
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
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<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
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<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
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<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
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<li><a href="/cgspace-notes/2023-11/">November, 2023</a></li>
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<h4>Links</h4>
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<ol class="list-unstyled">
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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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