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444 lines
17 KiB
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<body>
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<div class="blog-masthead">
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<a class="nav-link active" href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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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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<div class="col-sm-8 blog-main">
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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/2022-03/">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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<header>
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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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<header>
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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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<article class="blog-post">
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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="/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="2021-06-01">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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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
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<li><a href="/cgspace-notes/2022-02/">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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<li><a href="/cgspace-notes/2021-11/">November, 2021</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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