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435 lines
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<a class="nav-link active" 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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<div class="row">
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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/2022-03/">March, 2022</a></h2>
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<p class="blog-post-meta"><time datetime="2022-03-01T16:46:54+03:00">Tue Mar 01, 2022</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2022-03-01">2022-03-01</h2>
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<ul>
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<li>Send Gaia the last batch of potential duplicates for items 701 to 980:</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 id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv
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</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -o /tmp/2022-03-01-tac-batch4-701-980.csv
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</span></span><span style="display:flex;"><span>$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv
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</span></span><span style="display:flex;"><span>$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv > /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
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</span></span></code></pre></div>
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<a href='https://alanorth.github.io/cgspace-notes/2022-03/'>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/2022-03/">April, 2022</a></h2>
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<p class="blog-post-meta"><time datetime="2022-03-01T10:53:39+03:00">Tue Mar 01, 2022</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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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’s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc) Looking at the Solr statistics for 2022-03 on CGSpace I see 54.
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<a href='https://alanorth.github.io/cgspace-notes/2022-03/'>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/2022-02/">February, 2022</a></h2>
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<p class="blog-post-meta"><time datetime="2022-02-01T14:06:54+02:00">Tue Feb 01, 2022</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2022-02-01">2022-02-01</h2>
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<ul>
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<li>Meeting with Peter and Abenet about CGSpace in the One CGIAR
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<ul>
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<li>We agreed to buy $5,000 worth of credits from Atmire for future upgrades</li>
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<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>
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<li>We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one</li>
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<li>We agreed to try to do more alignment of affiliations/funders with ROR</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/2022-02/'>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/2022-01/">January, 2022</a></h2>
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<p class="blog-post-meta"><time datetime="2022-01-01T15:20:54+02:00">Sat Jan 01, 2022</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2022-01-01">2022-01-01</h2>
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<ul>
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<li>Start a full harvest on AReS</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2022-01/'>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/2021-12/">December, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-12-01T16:07:07+02:00">Wed Dec 01, 2021</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-12-01">2021-12-01</h2>
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<ul>
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<li>Atmire merged some changes I had submitted to the COUNTER-Robots project</li>
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<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>
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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>$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
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</span></span><span style="display:flex;"><span>Purging 1989 hits from The Knowledge AI in statistics
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</span></span><span style="display:flex;"><span>Purging 1235 hits from MaCoCu in statistics
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</span></span><span style="display:flex;"><span>Purging 455 hits from WhatsApp in statistics
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 3679
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</span></span></code></pre></div>
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<a href='https://alanorth.github.io/cgspace-notes/2021-12/'>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/2021-11/">November, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-11-02T22:27:07+02:00">Tue Nov 02, 2021</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-11-02">2021-11-02</h2>
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<ul>
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<li>I experimented with manually sharding the Solr statistics on DSpace Test</li>
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<li>First I exported all the 2019 stats from 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-console" data-lang="console"><span style="display:flex;"><span>$ ./run.sh -s http://localhost:8081/solr/statistics -f <span style="color:#e6db74">'time:2019-*'</span> -a export -o statistics-2019.json -k uid
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</span></span><span style="display:flex;"><span>$ zstd statistics-2019.json
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</span></span></code></pre></div>
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<a href='https://alanorth.github.io/cgspace-notes/2021-11/'>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/2021-10/">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="/cgspace-notes/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="/cgspace-notes/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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<header>
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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="/cgspace-notes/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="/cgspace-notes/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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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
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<li><a href="/cgspace-notes/2022-03/">April, 2022</a></li>
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<li><a href="/cgspace-notes/2022-02/">February, 2022</a></li>
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<li><a href="/cgspace-notes/2022-01/">January, 2022</a></li>
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<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>
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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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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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