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Delete duplicate metadata as described in my DSpace issue from last year: https://github.com/DSpace/DSpace/issues/8253
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Lower case all the AGROVOC subjects on CGSpace
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<meta name="twitter:description" content="2024-02-05
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Delete duplicate metadata as described in my DSpace issue from last year: https://github.com/DSpace/DSpace/issues/8253
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Lower case all the AGROVOC subjects on CGSpace
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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/2024-02/">February, 2024</a></h2>
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<time datetime="2024-02-05T11:10:00+03:00">Mon Feb 05, 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="2024-02-05">2024-02-05</h2>
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<ul>
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<li>Delete duplicate metadata as described in my DSpace issue from last year: <a href="https://github.com/DSpace/DSpace/issues/8253">https://github.com/DSpace/DSpace/issues/8253</a></li>
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<li>Lower case all the AGROVOC subjects on CGSpace</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>dspace<span style="color:#f92672">=#</span> <span style="color:#66d9ef">BEGIN</span>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>
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</span></span><span style="display:flex;"><span>dspace<span style="color:#f92672">=*#</span> <span style="color:#66d9ef">UPDATE</span> metadatavalue <span style="color:#66d9ef">SET</span> text_value<span style="color:#f92672">=</span><span style="color:#66d9ef">LOWER</span>(text_value) <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> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">187</span> <span style="color:#66d9ef">AND</span> text_value <span style="color:#f92672">~</span> <span style="color:#e6db74">'[[:upper:]]'</span>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">UPDATE</span> <span style="color:#ae81ff">180</span>
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</span></span><span style="display:flex;"><span>dspace<span style="color:#f92672">=*#</span> <span style="color:#66d9ef">COMMIT</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><h2 id="2024-02-06">2024-02-06</h2>
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<ul>
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<li>Discuss IWMI using the CGSpace REST API for their new website</li>
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<li>Export the IWMI community to extract their ORCID identifiers:</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 metadata-export -i 10568/16814 -f /tmp/iwmi.csv
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</span></span><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'cg.creator.identifier,cg.creator.identifier[en_US]'</span> ~/Downloads/2024-02-06-iwmi.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' \
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</span></span><span style="display:flex;"><span> | sort -u \
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</span></span><span style="display:flex;"><span> | tee /tmp/iwmi-orcids.txt \
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</span></span><span style="display:flex;"><span> | wc -l
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</span></span><span style="display:flex;"><span>353
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</span></span><span style="display:flex;"><span>$ ./ilri/resolve_orcids.py -i /tmp/iwmi-orcids.txt -o /tmp/iwmi-orcids-names.csv -d
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</span></span></code></pre></div><ul>
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<li>I noticed some similar looking names in our list so I clustered them in OpenRefine and manually checked a dozen or so to update our list</li>
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</ul>
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<h2 id="2024-02-07">2024-02-07</h2>
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<ul>
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<li>Maria asked me about the “missing” item from last week again
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<ul>
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<li>I can see it when I used the Admin search, but not in her workflow</li>
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<li>It was submitted by TIP so I checked that user’s workspace and found it there</li>
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<li>After depositing, it went into the workflow so Maria should be able to see it now</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-02-09">2024-02-09</h2>
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<ul>
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<li>Minor edits to CGSpace submission form</li>
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<li>Upload 55 ISNAR book chapters to CGSpace from Peter</li>
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</ul>
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<h2 id="2024-02-19">2024-02-19</h2>
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<ul>
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<li>Looking into the collection mapping issue on CGSpace
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<ul>
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<li>It seems to be by design in DSpace 7: <a href="https://github.com/DSpace/dspace-angular/issues/1203">https://github.com/DSpace/dspace-angular/issues/1203</a></li>
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<li>This is a massive setback for us…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-02-20">2024-02-20</h2>
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<ul>
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<li>Minor work on OpenRXV to fix a bug in the ng-select drop downs</li>
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<li>Minor work on the DSpace 7 nginx configuration to allow requesting robots.txt and sitemaps without hitting rate limits</li>
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</ul>
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<h2 id="2024-02-21">2024-02-21</h2>
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<ul>
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<li>Minor updates on OpenRXV, including one bug fix for missing mapped collections
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<ul>
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<li>Salem had to re-work the harvester for DSpace 7 since the mapped collections and parent collection list are separate!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-02-22">2024-02-22</h2>
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<ul>
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<li>Discuss tagging of datasets and re-work the submission form to encourage use of DOI field for any item that has a DOI, and the normal URL field if not
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<ul>
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<li>The “cg.identifier.dataurl” field will be used for “related” datasets</li>
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<li>I still have to check and move some metadata for existing datasets</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-02-23">2024-02-23</h2>
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<ul>
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<li>This morning Tomcat died due to an OOM kill from the kernel:</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>kernel: Out of memory: Killed process 698 (java) total-vm:14151300kB, anon-rss:9665812kB, file-rss:320kB, shmem-rss:0kB, UID:997 pgtables:20436kB oom_score_adj:0
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</span></span></code></pre></div><ul>
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<li>I don’t see any abnormal pattern in my Grafana graphs, for JVM or system load… very weird</li>
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<li>I updated the submission form on CGSpace to include the new changes to URLs for datasets
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<ul>
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<li>I also updated about 80 datasets to move the URLs to the correct field</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-02-25">2024-02-25</h2>
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<ul>
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<li>This morning Tomcat died while I was doing a CSV export, with an OOM kill from the kernel:</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>kernel: Out of memory: Killed process 720768 (java) total-vm:14079976kB, anon-rss:9301684kB, file-rss:152kB, shmem-rss:0kB, UID:997 pgtables:19488kB oom_score_adj:0
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</span></span></code></pre></div><ul>
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<li>I don’t know why this is happening so often recently…</li>
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</ul>
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<h2 id="2024-02-27">2024-02-27</h2>
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<ul>
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<li>IFPRI sent me a list of authors to add to our list for now, until we can find a better way of doing it
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<ul>
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<li>I extracted the existing authors from our controlled vocabulary and combined them with IFPRI’s:</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>$ xmllint --xpath <span style="color:#e6db74">'//node/isComposedBy/node()'</span> dspace/config/controlled-vocabularies/dc-contributor-author.xml <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | grep -oE 'label=".*"' \
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</span></span><span style="display:flex;"><span> | sed -e 's/label="//' -e 's/"$//' > /tmp/authors
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</span></span><span style="display:flex;"><span>$ cat /tmp/authors /tmp/ifpri-authors | sort -u > /tmp/new-authors
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</span></span></code></pre></div><h2 id="2024-02-28">2024-02-28</h2>
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<ul>
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<li>I figured out a way to add a new Angular component to handle all our relation fields</li>
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</ul>
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<h2 id="2024-02-29">2024-02-29</h2>
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<ul>
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<li>Clean up a bunch of metadata on CGSpace</li>
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</ul>
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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/2024-05/">May, 2024</a></li>
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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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<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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