<!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="2021-09-04T21:16:03+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 0.87.0" />
<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": "2021-09-01T09:14:07+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.ffbfea088a9a1666ec65c3a8cb4906e2a0e4f92dc70dbbf400a125ad2422123a.js" integrity="sha256-/7/qCIqaFmbsZcOoy0kG4qDk+S3HDbv0AKElrSQiEjo=" 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/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>
<pre><code class="language-console" data-lang="console"># docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
</code></pre><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>
<pre><code class="language-console" data-lang="console">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;
COPY 20994
</code></pre>
<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>
<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="/cgspace-notes/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="/cgspace-notes/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="/cgspace-notes/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="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/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="/cgspace-notes/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>
<pre><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
{
"count" : 100875,
"_shards" : {
"total" : 1,
"successful" : 1,
"skipped" : 0,
"failed" : 0
}
}
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2021-02/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-01/">January, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-01-03T10:13:54+02:00">Sun Jan 03, 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="2021-01-03">2021-01-03</h2>
<ul>
<li>Peter notified me that some filters on AReS were broken again
<ul>
<li>It’s the same issue with the field names getting <code>.keyword</code> appended to the end that I already <a href="https://github.com/ilri/OpenRXV/issues/66">filed an issue on OpenRXV about last month</a></li>
<li>I fixed the broken filters (careful to not edit any others, lest they break too!)</li>
</ul>
</li>
<li>Fix an issue with start page number for the DSpace REST API and statistics API in OpenRXV
<ul>
<li>The start page had been “1” in the UI, but in the backend they were doing some gymnastics to adjust to the zero-based offset/limit/page of the DSpace REST API and the statistics API</li>
<li>I adjusted it to default to 0 and added a note to the admin screen</li>
<li>I realized that this issue was actually causing the first page of 100 statistics to be missing…</li>
<li>For example, <a href="https://cgspace.cgiar.org/handle/10568/66839">this item</a> has 51 views on CGSpace, but 0 on AReS</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2021-01/'>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/2021-09/">September, 2021</a></li>
<li><a href="/cgspace-notes/2021-08/">August, 2021</a></li>
<li><a href="/cgspace-notes/2021-07/">July, 2021</a></li>
<li><a href="/cgspace-notes/2021-06/">June, 2021</a></li>
<li><a href="/cgspace-notes/2021-05/">May, 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>