cgspace-notes/docs/2022-12/index.html

286 lines
12 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="December, 2022" />
<meta property="og:description" content="2022-12-01
Fix some incorrect regions on CGSpace
I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions
Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!
Replace &ldquo;East Asia&rdquo; with &ldquo;Eastern Asia&rdquo; region on CGSpace (UN M.49 region)
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-12/" />
<meta property="article:published_time" content="2022-12-01T08:52:36+03:00" />
<meta property="article:modified_time" content="2022-12-04T03:19:49+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="December, 2022"/>
<meta name="twitter:description" content="2022-12-01
Fix some incorrect regions on CGSpace
I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions
Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!
Replace &ldquo;East Asia&rdquo; with &ldquo;Eastern Asia&rdquo; region on CGSpace (UN M.49 region)
"/>
<meta name="generator" content="Hugo 0.108.0">
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "BlogPosting",
"headline": "December, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-12/",
"wordCount": "617",
"datePublished": "2022-12-01T08:52:36+03:00",
"dateModified": "2022-12-04T03:19:49+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
},
"keywords": "Notes"
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2022-12/">
<title>December, 2022 | CGSpace Notes</title>
<!-- combined, minified CSS -->
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F&#43;GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" 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&#43;lcnA=" crossorigin="anonymous"></script>
<!-- RSS 2.0 feed -->
</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/2022-12/">December, 2022</a></h2>
<p class="blog-post-meta">
<time datetime="2022-12-01T08:52:36+03:00">Thu Dec 01, 2022</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2022-12-01">2022-12-01</h2>
<ul>
<li>Fix some incorrect regions on CGSpace
<ul>
<li>I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions</li>
</ul>
</li>
<li>Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!</li>
<li>Replace &ldquo;East Asia&rdquo; with &ldquo;Eastern Asia&rdquo; region on CGSpace (UN M.49 region)</li>
</ul>
<ul>
<li>CGSpace and PRMS information session with Enrico and a bunch of researchers</li>
<li>I noticed some minor issues with SPDX licenses and AGROVOC terms in items submitted by TIP so I sent a message to Daniel from Alliance</li>
<li>I startd a harvest on AReS since we&rsquo;ve updated so much metadata recently</li>
</ul>
<h2 id="2022-12-02">2022-12-02</h2>
<ul>
<li>File some issues related to metadata on the MEL issue tracker
<ul>
<li><a href="https://github.com/CodeObia/MEL/issues/11066">Only use &ldquo;Open Access&rdquo; or &ldquo;Limited Access&rdquo; access rights when publishing items on CGSpace</a></li>
<li><a href="https://github.com/CodeObia/MEL/issues/11067">Set the description when submitting bitstreams to CGSpace</a></li>
<li><a href="https://github.com/CodeObia/MEL/issues/11068">Some items have a Creative Commons license, but are Limited Access and bitstreams are locked</a></li>
</ul>
</li>
</ul>
<h2 id="2022-12-03">2022-12-03</h2>
<ul>
<li>I downloaded a fresh copy of CLARISA&rsquo;s institutions list as well as ROR&rsquo;s latest dump from 2022-12-01 to check how many are matching:</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 https://api.clarisa.cgiar.org/api/institutions | json_pp &gt; ~/Downloads/2022-12-03-CLARISA-institutions.json
</span></span><span style="display:flex;"><span>$ jq -r <span style="color:#e6db74">&#39;.[] | .name&#39;</span> ~/Downloads/2022-12-03-CLARISA-institutions.json &gt; ~/Downloads/2022-12-03-CLARISA-institutions.txt
</span></span><span style="display:flex;"><span>$ ./ilri/ror-lookup.py -i ~/Downloads/2022-12-03-CLARISA-institutions.txt -o /tmp/clarisa-ror-matches.csv -r v1.15-2022-12-01-ror-data.json
</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/clarisa-ror-matches.csv | wc -l
</span></span><span style="display:flex;"><span>1864
</span></span><span style="display:flex;"><span>$ wc -l ~/Downloads/2022-12-03-CLARISA-institutions.txt
</span></span><span style="display:flex;"><span>7060 /home/aorth/Downloads/2022-12-03-CLARISA-institutions.txt
</span></span></code></pre></div><ul>
<li>Out of the box they match 26.4%, but there are many institutions with multiple languages in the text value, as well as countries in parentheses so I think it could be higher</li>
<li>If I replace the slashes and remove the countries at the end there are slightly more matches, around 29%:</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>$ sed -e <span style="color:#e6db74">&#39;s_ / _\n_&#39;</span> -e <span style="color:#e6db74">&#39;s_/_\n_&#39;</span> -e <span style="color:#e6db74">&#39;s/ \?(.*)$//&#39;</span> ~/Downloads/2022-12-03-CLARISA-institutions.txt &gt; ~/Downloads/2022-12-03-CLARISA-institutions-alan.txt
</span></span></code></pre></div><ul>
<li>I checked CGSpace&rsquo;s top 1,000 affiliations too, first exporting from PostgreSQL:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT text_value as &#34;cg.contributor.affiliation&#34;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1000) to /tmp/2022-11-22-affiliations.csv;
</span></span></code></pre></div><ul>
<li>Then cutting (tab is the default delimeter):</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ cut -f <span style="color:#ae81ff">1</span> /tmp/2022-11-22-affiliations.csv &gt; 2022-11-22-affiliations.txt
</span></span><span style="display:flex;"><span>$ ./ilri/ror-lookup.py -i 2022-11-22-affiliations.txt -o /tmp/cgspace-matches.csv -r v1.15-2022-12-01-ror-data.json
</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/cgspace-matches.csv | wc -l
</span></span><span style="display:flex;"><span>542
</span></span></code></pre></div><ul>
<li>So that&rsquo;s a 54% match for our top affiliations</li>
<li>I realized we should actually check affiliations and sponsors, since those are stored in separate fields
<ul>
<li>When I add those the matches go down a bit to 45%</li>
</ul>
</li>
<li>Oh man, I realized institutions like <code>Université d'Abomey Calavi</code> don&rsquo;t match in ROR because they are like this in the JSON:</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>&#34;name&#34;: &#34;Universit\u00e9 d&#39;Abomey-Calavi&#34;
</span></span></code></pre></div><ul>
<li>So we likely match a bunch more than 50%&hellip;</li>
<li>I exported a list of affiliations and donors from CGSpace for Peter to look over and send corrections</li>
</ul>
<h2 id="2022-12-05">2022-12-05</h2>
<ul>
<li>First day of PRMS technical workshop in Rome</li>
<li>Last night I submitted a CSV import with changes to 1,500 Alliance items (adding regions) and it hadn&rsquo;t completed after twenty-four hours so I canceled it
<ul>
<li>Not sure if there is some rollback that will happen or what state the database will be in, so I will wait a few hours to see what happens before trying to modify those items again</li>
<li>I started it again a few hours later with a subset of the items and 4GB of RAM instead of 2</li>
<li>It completed successfully&hellip;</li>
</ul>
</li>
</ul>
<h2 id="2022-12-07">2022-12-07</h2>
<ul>
<li>I found a bug in my csv-metadata-quality script regarding the regions
<ul>
<li>I was accidentally checking <code>cg.coverage.subregion</code> due to a sloppy regex</li>
<li>This means I&rsquo;ve added a few thousand UN M.49 regions to the <code>cg.coverage.subregion</code> field in the last few days</li>
<li>I had to extract them from CGSpace and delete them using <code>delete-metadata-values.py</code></li>
</ul>
</li>
<li>My <a href="https://github.com/DSpace/DSpace/pull/8550">DSpace 7.x pull request to tell ImageMagick about the PDF CropBox</a> was merged</li>
</ul>
<!-- raw HTML omitted -->
</article>
</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/2022-12/">December, 2022</a></li>
<li><a href="/cgspace-notes/2022-11/">November, 2022</a></li>
<li><a href="/cgspace-notes/2022-10/">October, 2022</a></li>
<li><a href="/cgspace-notes/2022-09/">September, 2022</a></li>
<li><a href="/cgspace-notes/2022-08/">August, 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>