mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-23 07:00:20 +01:00
459 lines
17 KiB
HTML
459 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="Posts" />
|
|
<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/posts/" />
|
|
<meta property="og:updated_time" content="2022-08-13T21:51:49-07:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="Posts"/>
|
|
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
|
<meta name="generator" content="Hugo 0.101.0" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "Blog",
|
|
"headline": "CGSpace Notes",
|
|
"url" : "https://alanorth.github.io/cgspace-notes/posts/",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"dateModified": "2022-08-01T10:22:36+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/posts/">
|
|
|
|
<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/posts/index.xml" title="CGSpace Notes" />
|
|
|
|
|
|
|
|
|
|
</head>
|
|
|
|
<body>
|
|
|
|
|
|
<div class="blog-masthead">
|
|
<div class="container">
|
|
<nav class="nav blog-nav">
|
|
<a class="nav-link " 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/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="/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="/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="/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="/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="/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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-05/">May, 2021</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2021-05-02T09:50:54+03:00">Sun May 02, 2021</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2021-05-01">2021-05-01</h2>
|
|
<ul>
|
|
<li>I looked at the top user agents and IPs in the Solr statistics for last month and I see these user agents:
|
|
<ul>
|
|
<li>“RI/1.0”, 1337</li>
|
|
<li>“Microsoft Office Word 2014”, 941</li>
|
|
</ul>
|
|
</li>
|
|
<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>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2021-05/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-04/">April, 2021</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2021-04-01T09:50:54+03:00">Thu Apr 01, 2021</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2021-04-01">2021-04-01</h2>
|
|
<ul>
|
|
<li>I wrote a script to query Sherpa’s API for our ISSNs: <code>sherpa-issn-lookup.py</code>
|
|
<ul>
|
|
<li>I’m curious to see how the results compare with the results from Crossref yesterday</li>
|
|
</ul>
|
|
</li>
|
|
<li>AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
|
|
<ul>
|
|
<li>I simply took everything down with docker-compose and then back up, and then it was OK</li>
|
|
<li>Perhaps one of the containers crashed, I should have looked closer but I was in a hurry</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2021-04/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-03/">March, 2021</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2021-03-01T10:13:54+02:00">Mon Mar 01, 2021</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2021-03-01">2021-03-01</h2>
|
|
<ul>
|
|
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
|
|
<ul>
|
|
<li>He’s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
|
|
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2021-03/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2021-02-21T13:27:35+02:00">Sun Feb 21, 2021</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/migration/" rel="tag">Migration</a>
|
|
|
|
</p>
|
|
</header>
|
|
<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>
|
|
<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>
|
|
<a href='https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2021-02-01T10:13:54+02:00">Mon Feb 01, 2021</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2021-02-01">2021-02-01</h2>
|
|
<ul>
|
|
<li>Abenet said that CIP found more duplicate records in their export from AReS
|
|
<ul>
|
|
<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>
|
|
<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>
|
|
</ul>
|
|
</li>
|
|
<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
|
|
<li>Check the results of the AReS harvesting from last night:</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>$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'</span>
|
|
</span></span><span style="display:flex;"><span>{
|
|
</span></span><span style="display:flex;"><span> "count" : 100875,
|
|
</span></span><span style="display:flex;"><span> "_shards" : {
|
|
</span></span><span style="display:flex;"><span> "total" : 1,
|
|
</span></span><span style="display:flex;"><span> "successful" : 1,
|
|
</span></span><span style="display:flex;"><span> "skipped" : 0,
|
|
</span></span><span style="display:flex;"><span> "failed" : 0
|
|
</span></span><span style="display:flex;"><span> }
|
|
</span></span><span style="display:flex;"><span>}
|
|
</span></span></code></pre></div>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2021-02/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
<nav class="blog-pagination">
|
|
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/" rel="prev" role="button">Previous page</a>
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/3/" 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/2022-08/">August, 2022</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2022-07/">July, 2022</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2022-06/">June, 2022</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2022-04/">April, 2022</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>
|