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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/2022-03/">March, 2022</a></h2>
<p class="blog-post-meta"><time datetime="2022-03-01T16:46:54+03:00">Tue Mar 01, 2022</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2022-03-01">2022-03-01</h2>
<ul>
<li>Send Gaia the last batch of potential duplicates for items 701 to 980:</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 id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv &gt; /tmp/tac4.csv
</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p <span style="color:#e6db74">&#39;fuuu&#39;</span> -o /tmp/2022-03-01-tac-batch4-701-980.csv
</span></span><span style="display:flex;"><span>$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv &gt; /tmp/tac4-filenames.csv
</span></span><span style="display:flex;"><span>$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv &gt; /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2022-03/'>Read more →</a>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-03/">April, 2022</a></h2>
<p class="blog-post-meta"><time datetime="2022-03-01T10:53:39+03:00">Tue Mar 01, 2022</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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2022-04-01 I did G1GC tests on DSpace Test (linode26) to compliment the CMS tests I did yesterday The Discovery indexing took this long: real 334m33.625s user 227m51.331s sys 3m43.037s 2022-04-04 Start a full harvest on AReS Help Marianne with submit/approve access on a new collection on CGSpace Go back in Gaia&rsquo;s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc)
<a href='https://alanorth.github.io/cgspace-notes/2022-03/'>Read more →</a>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-02/">February, 2022</a></h2>
<p class="blog-post-meta"><time datetime="2022-02-01T14:06:54+02:00">Tue Feb 01, 2022</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
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<h2 id="2022-02-01">2022-02-01</h2>
<ul>
<li>Meeting with Peter and Abenet about CGSpace in the One CGIAR
<ul>
<li>We agreed to buy $5,000 worth of credits from Atmire for future upgrades</li>
<li>We agreed to move CRPs and non-CGIAR communities off the home page, as well as some other things for the CGIAR System Organization</li>
<li>We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one</li>
<li>We agreed to try to do more alignment of affiliations/funders with ROR</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2022-02/'>Read more →</a>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-01/">January, 2022</a></h2>
<p class="blog-post-meta"><time datetime="2022-01-01T15:20:54+02:00">Sat Jan 01, 2022</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2022-01-01">2022-01-01</h2>
<ul>
<li>Start a full harvest on AReS</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2022-01/'>Read more →</a>
</article>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-12/">December, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-12-01T16:07:07+02:00">Wed Dec 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
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<h2 id="2021-12-01">2021-12-01</h2>
<ul>
<li>Atmire merged some changes I had submitted to the COUNTER-Robots project</li>
<li>I updated our local spider user agents and then re-ran the list with my <code>check-spider-hits.sh</code> script on CGSpace:</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>$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
</span></span><span style="display:flex;"><span>Purging 1989 hits from The Knowledge AI in statistics
</span></span><span style="display:flex;"><span>Purging 1235 hits from MaCoCu in statistics
</span></span><span style="display:flex;"><span>Purging 455 hits from WhatsApp in statistics
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 3679
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-12/'>Read more →</a>
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<article class="blog-post">
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-11/">November, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-11-02T22:27:07+02:00">Tue Nov 02, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-11-02">2021-11-02</h2>
<ul>
<li>I experimented with manually sharding the Solr statistics on DSpace Test</li>
<li>First I exported all the 2019 stats from CGSpace:</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>$ ./run.sh -s http://localhost:8081/solr/statistics -f <span style="color:#e6db74">&#39;time:2019-*&#39;</span> -a export -o statistics-2019.json -k uid
</span></span><span style="display:flex;"><span>$ zstd statistics-2019.json
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-11/'>Read more →</a>
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<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-10/">October, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-10-01T11:14:07+03:00">Fri Oct 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-10-01">2021-10-01</h2>
<ul>
<li>Export all affiliations on CGSpace and run them against the latest RoR data dump:</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>localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &#34;cg.contributor.affiliation&#34;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>$ csvcut -c <span style="color:#ae81ff">1</span> /tmp/2021-10-01-affiliations.csv | sed 1d &gt; /tmp/2021-10-01-affiliations.txt
</span></span><span style="display:flex;"><span>$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
</span></span><span style="display:flex;"><span>ations-matching.csv
</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
</span></span><span style="display:flex;"><span>1879
</span></span><span style="display:flex;"><span>$ wc -l /tmp/2021-10-01-affiliations.txt
</span></span><span style="display:flex;"><span>7100 /tmp/2021-10-01-affiliations.txt
</span></span></code></pre></div><ul>
<li>So we have 1879/7100 (26.46%) matching already</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-10/'>Read more →</a>
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<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-09/">September, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-09-01T09:14:07+03:00">Wed Sep 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-09-02">2021-09-02</h2>
<ul>
<li>Troubleshooting the missing Altmetric scores on AReS
<ul>
<li>Turns out that I didn&rsquo;t actually fix them last month because the check for <code>content.altmetric</code> still exists, and I can&rsquo;t access the DOIs using <code>_h.source.DOI</code> for some reason</li>
<li>I can access all other kinds of item metadata using the Elasticsearch label, but not DOI!!!</li>
<li>I will change <code>DOI</code> to <code>tomato</code> in the repository setup and start a re-harvest&hellip; I need to see if this is some kind of reserved word or something&hellip;</li>
<li>Even as <code>tomato</code> I can&rsquo;t access that field as <code>_h.source.tomato</code> in Angular, but it does work as a filter source&hellip; sigh</li>
</ul>
</li>
<li>I&rsquo;m having problems using the OpenRXV API
<ul>
<li>The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search query properly&hellip;</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-09/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-08/">August, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-08-01T09:01:07+03:00">Sun Aug 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-08-01">2021-08-01</h2>
<ul>
<li>Update Docker images on AReS server (linode20) and reboot the server:</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># docker images | grep -v ^REPO | sed <span style="color:#e6db74">&#39;s/ \+/:/g&#39;</span> | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
</span></span></code></pre></div><ul>
<li>I decided to upgrade linode20 from Ubuntu 18.04 to 20.04</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-08/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-07/">July, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-07-01T08:53:07+03:00">Thu Jul 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-07-01">2021-07-01</h2>
<ul>
<li>Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVOC for Enrico:</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>localhost/dspace63= &gt; \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242, 187) GROUP BY subject ORDER BY count DESC) to /tmp/2021-07-01-all-subjects.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>COPY 20994
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-07/'>Read more →</a>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
<li><a href="/cgspace-notes/2022-03/">April, 2022</a></li>
<li><a href="/cgspace-notes/2022-02/">February, 2022</a></li>
<li><a href="/cgspace-notes/2022-01/">January, 2022</a></li>
<li><a href="/cgspace-notes/2021-12/">December, 2021</a></li>
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<h4>Links</h4>
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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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