mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-27 23:44:30 +01:00
444 lines
17 KiB
HTML
444 lines
17 KiB
HTML
<!DOCTYPE html>
|
|
<html lang="en" >
|
|
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
|
|
|
|
|
<meta property="og:title" content="CGSpace Notes" />
|
|
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
|
<meta property="og:type" content="website" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
|
|
<meta property="og:updated_time" content="2022-03-04T15:30:06+03:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="CGSpace Notes"/>
|
|
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
|
<meta name="generator" content="Hugo 0.93.1" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "Blog",
|
|
"headline": "CGSpace Notes",
|
|
"url" : "https://alanorth.github.io/cgspace-notes/",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"dateModified": "2022-03-01T16:46:54+03:00",
|
|
"keywords": "notes, migration, notes",
|
|
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
|
|
}
|
|
</script>
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/">
|
|
|
|
<title>CGSpace Notes</title>
|
|
|
|
|
|
<!-- combined, minified CSS -->
|
|
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.beb8012edc08ba10be012f079d618dc243812267efe62e11f22fe49618f976a4.css" rel="stylesheet" integrity="sha256-vrgBLtwIuhC+AS8HnWGNwkOBImfv5i4R8i/klhj5dqQ=" crossorigin="anonymous">
|
|
|
|
|
|
<!-- minified Font Awesome for SVG icons -->
|
|
|
|
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
|
|
|
|
<!-- RSS 2.0 feed -->
|
|
<link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" />
|
|
|
|
|
|
|
|
|
|
</head>
|
|
|
|
<body>
|
|
|
|
|
|
<div class="blog-masthead">
|
|
<div class="container">
|
|
<nav class="nav blog-nav">
|
|
<a class="nav-link active" href="https://alanorth.github.io/cgspace-notes/">Home</a>
|
|
</nav>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
|
|
|
|
<header class="blog-header">
|
|
<div class="container">
|
|
<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>
|
|
</div>
|
|
</header>
|
|
|
|
|
|
|
|
|
|
<div class="container">
|
|
<div class="row">
|
|
<div class="col-sm-8 blog-main">
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<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> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<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 > /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">'fuuu'</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 > /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 > /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>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<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> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<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>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<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> <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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<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> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<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>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<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> <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">'time:2019-*'</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>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<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> <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= > \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;
|
|
</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
|
|
</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>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<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> <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’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>
|
|
<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… I need to see if this is some kind of reserved word or something…</li>
|
|
<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>
|
|
</ul>
|
|
</li>
|
|
<li>I’m having problems using the OpenRXV API
|
|
<ul>
|
|
<li>The syntax Moayad showed me last month doesn’t seem to honor the search query properly…</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> <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">'s/ \+/:/g'</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> <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= > \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>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-06/">June, 2021</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2021-06-01T10:51:07+03:00">Tue Jun 01, 2021</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2021-06-01">2021-06-01</h2>
|
|
<ul>
|
|
<li>IWMI notified me that AReS was down with an HTTP 502 error
|
|
<ul>
|
|
<li>Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification</li>
|
|
<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>
|
|
<li>I simply started it and AReS was running again:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2021-06/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
<nav class="blog-pagination">
|
|
|
|
|
|
|
|
<a class="btn btn-outline-primary disabled" href="#" role="button" aria-disabled="true">Previous page</a>
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/page/2/" rel="next" role="button">Next page</a>
|
|
|
|
</nav>
|
|
|
|
|
|
|
|
|
|
|
|
</div> <!-- /.blog-main -->
|
|
|
|
<aside class="col-sm-3 ml-auto blog-sidebar">
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
|
|
<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2022-02/">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>
|
|
|
|
<li><a href="/cgspace-notes/2021-11/">November, 2021</a></li>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Links</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
<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>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
</aside>
|
|
|
|
|
|
</div> <!-- /.row -->
|
|
</div> <!-- /.container -->
|
|
|
|
|
|
|
|
<footer class="blog-footer">
|
|
<p dir="auto">
|
|
|
|
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
|
|
|
</p>
|
|
<p>
|
|
<a href="#">Back to top</a>
|
|
</p>
|
|
</footer>
|
|
|
|
|
|
</body>
|
|
|
|
</html>
|