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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: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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<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><ul>
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<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>
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<li>Maria asked me for a CSV with all the broken Bioversity permalinks so I exported them for her:</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>$ 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">\
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</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
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</span></span></code></pre></div><h2 id="2024-03-12">2024-03-12</h2>
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<ul>
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<li>Run the duplicate checker for IFPRI 2023 batch upload</li>
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</ul>
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<h2 id="2024-03-13">2024-03-13</h2>
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<ul>
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<li>I found about 428 duplicates in the IFPRI 2023 batch records
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<ul>
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<li>Alarmingly, I found about 18 that are duplicated on CGSpace as well!</li>
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<li>I looked closer and decided that 11 were duplicates, so I merged the metadata and withdrew the later ones</li>
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</ul>
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</li>
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<li>Alliance asked me to get him the Handles for items submitted by TIP that are not discoverable
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<ul>
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<li>I found it easiest to use the <code>ds6_item2itemhandle</code> <a href="https://wiki.lyrasis.org/display/DSPACE/Helper+SQL+functions+for+DSpace+6">DSpace SQL helper function</a> with a nested query on the provenance:</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">SELECT</span> ds6_item2itemhandle(dspace_object_id) <span style="color:#66d9ef">AS</span> handle <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">WHERE</span> <span style="color:#66d9ef">NOT</span> discoverable) <span style="color:#66d9ef">AND</span> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">28</span> <span style="color:#66d9ef">AND</span> text_value <span style="color:#66d9ef">LIKE</span> <span style="color:#e6db74">'Submitted by Alliance TIP Submit%'</span>;
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</span></span></code></pre></div><h2 id="2024-03-14">2024-03-14</h2>
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<ul>
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<li>Looking in to reports of rate limiting of Altmetric’s bot on CGSpace
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<ul>
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<li>I don’t see any HTTP 429 responses for their user agents in any of our logs…</li>
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<li>I tried myself on an item page and never hit a limit…</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>$ <span style="color:#66d9ef">for</span> num in <span style="color:#f92672">{</span>1..60<span style="color:#f92672">}</span>; <span style="color:#66d9ef">do</span> echo -n <span style="color:#e6db74">"Request </span><span style="color:#e6db74">${</span>num<span style="color:#e6db74">}</span><span style="color:#e6db74">: "</span>; curl -s -o /dev/null -w <span style="color:#e6db74">"%{http_code}"</span> https://dspace7test.ilri.org/items/c9b8999d-3001-42ba-a267-14f4bfa90b53 <span style="color:#f92672">&&</span> echo; <span style="color:#66d9ef">done</span>
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</span></span><span style="display:flex;"><span>Request 1: 200
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</span></span><span style="display:flex;"><span>Request 2: 200
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</span></span><span style="display:flex;"><span>Request 3: 200
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</span></span><span style="display:flex;"><span>Request 4: 200
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</span></span><span style="display:flex;"><span>...
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</span></span><span style="display:flex;"><span>Request 60: 200
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</span></span></code></pre></div><ul>
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<li>All responses were HTTP 200…</li>
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<li>In any case, I whitelisted their production IPs and told them to try again</li>
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<li>I imported 468 of IFPRI’s 2023 records that were confirmed to not be duplicates to CGSpace
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<ul>
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<li>I also spent some time merging metadata from 415 of the remaining 432 duplicates with the metadata for the existing items on CGSpace</li>
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<li>This was a bit of dirty work using csvkit, xsv, and OpenRefine</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-03-17">2024-03-17</h2>
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<ul>
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<li>There are 17 records from IFPRI’s 2023 batch that are remaining from the 432 that I identified as already being on CGSpace
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<ul>
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<li>These are different in that they are duplicates on CGSpace as well, so the csvjoin failed and the metadata got messed up in my migration</li>
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<li>I looked closer and whittled this down to 14 actual records, and spent some time working on them</li>
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<li>I isolated 12 of these items that existed on CGSpace and added publication ranks, project identifiers, and provenance links</li>
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<li>Now there only remain two confusing records about the Inkomati catchment</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-03-18">2024-03-18</h2>
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<ul>
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<li>Checking to see how many IFPRI records we have migrated so far:</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>$ csvgrep -c <span style="color:#e6db74">'dc.description.provenance[en_US]'</span> -m <span style="color:#e6db74">'Original URL from IFPRI CONTENTdm'</span> cgspace.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],dc.description.provenance[en_US],dcterms.type[en_US]' \
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</span></span><span style="display:flex;"><span> | tee /tmp/ifpri-records.csv \
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</span></span><span style="display:flex;"><span> | csvstat --count
|
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</span></span><span style="display:flex;"><span>898
|
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</span></span></code></pre></div><ul>
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<li>I finalized the remaining two on Inkomati catchment and now we are at 900!</li>
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</ul>
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<h1 id="2024-03-19">2024-03-19</h1>
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<ul>
|
|
<li>IWMI sent me some new author ORCID identifiers so I updated our list</li>
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|
<li>Started working on updating my data for the Ontology CoP webinar on CGIAR and AGROVOC
|
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<ul>
|
|
<li>First extracting all unique subjects on CGSpace:</li>
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|
</ul>
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|
</li>
|
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</ul>
|
|
<pre tabindex="0"><code>localhost/dspace7= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS "subject" FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119)) to /tmp/2024-03-19-cgspace-subjects.csv WITH CSV HEADER;
|
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COPY 28024
|
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</code></pre><ul>
|
|
<li>Then I extracted the subjects and looked them up against AGROVOC:</li>
|
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</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 subject /tmp/2024-03-19-cgspace-subjects.csv | sed <span style="color:#e6db74">'1d'</span> > /tmp/2024-03-19-cgspace-subjects.txt
|
|
</span></span><span style="display:flex;"><span>$ ./ilri/agrovoc_lookup.py -i /tmp/2024-03-19-cgspace-subjects.txt -o /tmp/2024-03-19-cgspace-subjects-results.csv
|
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</span></span></code></pre></div><h2 id="2024-03-20">2024-03-20</h2>
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<ul>
|
|
<li>Identify seven duplicates on CGSpace from the PRMS results and withdraw them from CGSpace</li>
|
|
</ul>
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<h2 id="2024-03-21">2024-03-21</h2>
|
|
<ul>
|
|
<li>Look more closely at duplicates on CGSpace based on a fresh export
|
|
<ul>
|
|
<li>Using DOIs I found ~842 that occur more than once for journal articles alone, so probably around 400 duplicates</li>
|
|
<li>I did a handful of them, merging the metadata and withdrawing the duplicate, and decided to add <code>dcterms.replaces</code> with the handle in the original</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-03-22">2024-03-22</h2>
|
|
<ul>
|
|
<li>Look at duplicate DOIs on CGSpace and address a dozen or so</li>
|
|
</ul>
|
|
<h2 id="2024-03-23">2024-03-23</h2>
|
|
<ul>
|
|
<li>Look at duplicate DOIs on CGSpace and address a dozen or so</li>
|
|
<li>Update Tomcat and Solr to latest versions
|
|
<ul>
|
|
<li>I had done some tests with these last week, and did a last minute test on DSpace 7 Test to make sure submission and searching worked</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-03-24">2024-03-24</h2>
|
|
<ul>
|
|
<li>Slowly process several dozen more duplicate DOIs on CGSpace, sigh…</li>
|
|
</ul>
|
|
<h2 id="2024-03-26">2024-03-26</h2>
|
|
<ul>
|
|
<li>File an issue on dspace-angular about improving withdrawn item tombstones: <a href="https://github.com/DSpace/dspace-angular/issues/2880">https://github.com/DSpace/dspace-angular/issues/2880</a></li>
|
|
<li>Merge metadata and withdraw more duplicates on CGSpace</li>
|
|
</ul>
|
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</article>
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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/2024-04/">April, 2024</a></li>
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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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<section class="sidebar-module">
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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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|
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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