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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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<div class="container">
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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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</div>
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</header>
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<div class="container">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-10/">October, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-10-01T11:14:07+03:00">Fri Oct 01, 2021</time> by Alan Orth 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="2021-10-01">2021-10-01</h2>
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<ul>
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<li>Export all affiliations on CGSpace and run them against the latest RoR data dump:</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>localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", 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;
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</span></span><span style="display:flex;"><span>$ csvcut -c <span style="color:#ae81ff">1</span> /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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</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
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</span></span><span style="display:flex;"><span>ations-matching.csv
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</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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</span></span><span style="display:flex;"><span>1879
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</span></span><span style="display:flex;"><span>$ wc -l /tmp/2021-10-01-affiliations.txt
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</span></span><span style="display:flex;"><span>7100 /tmp/2021-10-01-affiliations.txt
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</span></span></code></pre></div><ul>
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<li>So we have 1879/7100 (26.46%) matching already</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-10/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-09/">September, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-09-01T09:14:07+03:00">Wed Sep 01, 2021</time> by Alan Orth 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="2021-09-02">2021-09-02</h2>
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<ul>
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<li>Troubleshooting the missing Altmetric scores on AReS
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<ul>
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<li>Turns out that I didn’t actually fix them last month because the check for <code>content.altmetric</code> still exists, and I can’t access the DOIs using <code>_h.source.DOI</code> for some reason</li>
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<li>I can access all other kinds of item metadata using the Elasticsearch label, but not DOI!!!</li>
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<li>I will change <code>DOI</code> to <code>tomato</code> in the repository setup and start a re-harvest… I need to see if this is some kind of reserved word or something…</li>
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<li>Even as <code>tomato</code> I can’t access that field as <code>_h.source.tomato</code> in Angular, but it does work as a filter source… sigh</li>
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</ul>
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</li>
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<li>I’m having problems using the OpenRXV API
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<ul>
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<li>The syntax Moayad showed me last month doesn’t seem to honor the search query properly…</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-09/'>Read more →</a>
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</article>
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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/2021-08/">August, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-08-01T09:01:07+03:00">Sun Aug 01, 2021</time> by Alan Orth 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="2021-08-01">2021-08-01</h2>
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<ul>
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<li>Update Docker images on AReS server (linode20) and reboot the server:</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># docker images | grep -v ^REPO | sed <span style="color:#e6db74">'s/ \+/:/g'</span> | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
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</span></span></code></pre></div><ul>
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<li>I decided to upgrade linode20 from Ubuntu 18.04 to 20.04</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-08/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-07/">July, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-07-01T08:53:07+03:00">Thu Jul 01, 2021</time> by Alan Orth 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="2021-07-01">2021-07-01</h2>
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<ul>
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<li>Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVOC for Enrico:</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>localhost/dspace63= > \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;
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</span></span><span style="display:flex;"><span>COPY 20994
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</span></span></code></pre></div>
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<a href='https://alanorth.github.io/cgspace-notes/2021-07/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-06/">June, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-06-01T10:51:07+03:00">Tue Jun 01, 2021</time> by Alan Orth 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="2021-06-01">2021-06-01</h2>
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<ul>
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<li>IWMI notified me that AReS was down with an HTTP 502 error
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<ul>
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<li>Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification</li>
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<li>I don’t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the <code>angular_nginx</code> container isn’t running</li>
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<li>I simply started it and AReS was running again:</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-06/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-05/">May, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-05-02T09:50:54+03:00">Sun May 02, 2021</time> by Alan Orth 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="2021-05-01">2021-05-01</h2>
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<ul>
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<li>I looked at the top user agents and IPs in the Solr statistics for last month and I see these user agents:
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<ul>
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<li>“RI/1.0”, 1337</li>
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<li>“Microsoft Office Word 2014”, 941</li>
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</ul>
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</li>
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<li>I will add the RI/1.0 pattern to our DSpace agents overload and purge them from Solr (we had previously seen this agent with 9,000 hits or so in 2020-09), but I think I will leave the Microsoft Word one… as that’s an actual user…</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-05/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-04/">April, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-04-01T09:50:54+03:00">Thu Apr 01, 2021</time> by Alan Orth 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="2021-04-01">2021-04-01</h2>
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<ul>
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<li>I wrote a script to query Sherpa’s API for our ISSNs: <code>sherpa-issn-lookup.py</code>
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<ul>
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<li>I’m curious to see how the results compare with the results from Crossref yesterday</li>
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</ul>
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</li>
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<li>AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
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<ul>
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<li>I simply took everything down with docker-compose and then back up, and then it was OK</li>
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<li>Perhaps one of the containers crashed, I should have looked closer but I was in a hurry</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-04/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-03/">March, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time> by Alan Orth 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="2021-03-01">2021-03-01</h2>
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<ul>
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<li>Discuss some OpenRXV issues with Abdullah from CodeObia
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<ul>
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<li>He’s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
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<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-03/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></h2>
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<p class="blog-post-meta"><time datetime="2021-02-21T13:27:35+02:00">Sun Feb 21, 2021</time> by Alan Orth 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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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/migration/" rel="tag">Migration</a>
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</p>
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</header>
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<p>Changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2. Implemented on 2021-02-21.</p>
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<p>With reference to <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2 draft standard</a> by Marie-Angélique as well as <a href="http://www.dublincore.org/specifications/dublin-core/dcmi-terms/">DCMI DCTERMS</a>.</p>
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<a href='https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-02-01T10:13:54+02:00">Mon Feb 01, 2021</time> by Alan Orth 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="2021-02-01">2021-02-01</h2>
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<ul>
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<li>Abenet said that CIP found more duplicate records in their export from AReS
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<ul>
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<li>I re-opened <a href="https://github.com/ilri/OpenRXV/issues/67">the issue</a> on OpenRXV where we had previously noticed this</li>
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<li>The shared link where the duplicates are is here: <a href="https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6">https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6</a></li>
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</ul>
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</li>
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<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
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<li>Check the results of the AReS harvesting from last night:</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>$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'</span>
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</span></span><span style="display:flex;"><span>{
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</span></span><span style="display:flex;"><span> "count" : 100875,
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</span></span><span style="display:flex;"><span> "_shards" : {
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</span></span><span style="display:flex;"><span> "total" : 1,
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</span></span><span style="display:flex;"><span> "successful" : 1,
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</span></span><span style="display:flex;"><span> "skipped" : 0,
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</span></span><span style="display:flex;"><span> "failed" : 0
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</span></span><span style="display:flex;"><span> }
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</span></span><span style="display:flex;"><span>}
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</span></span></code></pre></div>
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<a href='https://alanorth.github.io/cgspace-notes/2021-02/'>Read more →</a>
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</article>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2022-08/">August, 2022</a></li>
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<li><a href="/cgspace-notes/2022-07/">July, 2022</a></li>
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<li><a href="/cgspace-notes/2022-06/">June, 2022</a></li>
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<li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
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<li><a href="/cgspace-notes/2022-04/">April, 2022</a></li>
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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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