<!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="August, 2022" />
<meta property="og:description" content="2022-08-01
Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-08/" />
<meta property="article:published_time" content="2022-08-01T10:22:36+03:00" />
<meta property="article:modified_time" content="2022-08-01T16:36:13+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="August, 2022"/>
<meta name="twitter:description" content="2022-08-01
Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
"/>
<meta name="generator" content="Hugo 0.101.0" />
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "BlogPosting",
"headline": "August, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-08/",
"wordCount": "492",
"datePublished": "2022-08-01T10:22:36+03:00",
"dateModified": "2022-08-01T16:36:13+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
},
"keywords": "Notes"
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2022-08/">
<title>August, 2022 | 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 -->
</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/2022-08/">August, 2022</a></h2>
<p class="blog-post-meta">
<time datetime="2022-08-01T10:22:36+03:00">Mon Aug 01, 2022</time>
in
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2022-08-01">2022-08-01</h2>
<ul>
<li>Our request to add <a href="https://github.com/spdx/license-list-XML/issues/1525">CC-BY-3.0-IGO to SPDX</a> was approved a few weeks ago</li>
</ul>
<h2 id="2022-08-02">2022-08-02</h2>
<ul>
<li>Resume working on the MARLO Innovations
<ul>
<li>Last week Jose had sent me an updated CSV with UTF-8 formatting, which was missing the filename column</li>
<li>I joined it with the older file (stripped down to just the <code>cg.number</code> and <code>filename</code> columns and then did the same cleanups I had done last week</li>
<li>I noticed there are six PDFs unused, so I asked Jose</li>
</ul>
</li>
<li>Spent some time trying to understand the REST API submission issues that Rafael from CIAT is having with tip-approve and tip-submit
<ul>
<li>First, according to my notes in 2020-10, a user must be a <em>collection admin</em> in order to submit via the REST API</li>
<li>Second, a collection must have a “Accept/Reject/Edit Metadata” step defined in the workflow</li>
<li>Also, I referenced my notes from this gist I had made for exactly this purpose! <a href="https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a">https://gist.github.com/alanorth/40fc3092aefd78f978cca00e8abeeb7a</a></li>
</ul>
</li>
</ul>
<h2 id="2022-08-03">2022-08-03</h2>
<ul>
<li>I came up with an interesting idea to add missing countries and AGROVOC terms to the MARLO Innovation metadata
<ul>
<li>I copied the abstract column to two new fields: <code>countrytest</code> and <code>agrovoctest</code> and then used this Jython code as a transform to drop terms that don’t match (using CGSpace’s country list and list of 1,400 AGROVOC terms):</li>
</ul>
</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#66d9ef">with</span> open(<span style="color:#e6db74">r</span><span style="color:#e6db74">"/tmp/cgspace-countries.txt"</span>,<span style="color:#e6db74">'r'</span>) <span style="color:#66d9ef">as</span> f :
</span></span><span style="display:flex;"><span> countries <span style="color:#f92672">=</span> [name<span style="color:#f92672">.</span>rstrip()<span style="color:#f92672">.</span>lower() <span style="color:#66d9ef">for</span> name <span style="color:#f92672">in</span> f]
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> <span style="color:#e6db74">"||"</span><span style="color:#f92672">.</span>join([x <span style="color:#66d9ef">for</span> x <span style="color:#f92672">in</span> value<span style="color:#f92672">.</span>split(<span style="color:#e6db74">' '</span>) <span style="color:#66d9ef">if</span> x<span style="color:#f92672">.</span>lower() <span style="color:#f92672">in</span> countries])
</span></span></code></pre></div><ul>
<li>Then I joined them with the other country and AGROVOC columns
<ul>
<li>I had originally tried to use csv-metadata-quality to look up and drop invalid AGROVOC terms but it was timing out ever dozen or so requests</li>
<li>Then I briefly tried to use lightrdf to export a text file of labels from AGROVOC’s RDF, but I couldn’t figure it out</li>
<li>I just realized this will not match countries with spaces in our cell value, ugh… and Jython has weird syntax and errors and I can’t get normal Python code to work here, I’m missing something</li>
</ul>
</li>
<li>Then I extracted the titles, dates, and types and added IDs, then ran them through <code>check-duplicates.py</code> to find the existing items on CGSpace so I can add them as <code>dcterm.relation</code> links</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 -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-08-03-Innovations-Cleaned.csv | sed <span style="color:#e6db74">'1s/line_number/id/'</span> > /tmp/innovations-temp.csv
</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/innovations-temp.csv -u dspacetest -db dspacetest -p <span style="color:#e6db74">'dom@in34sniper'</span> -o /tmp/ccafs-duplicates.csv
</span></span></code></pre></div><ul>
<li>There were about 115 with existing items on CGSpace</li>
<li>Then I did some minor processing and checking of the duplicates file (for example, some titles appear more than once in both files), and joined with the other file (left join):</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>$ csvjoin --left -c dc.title ~/Downloads/2022-08-03-Innovations-Cleaned.csv ~/Downloads/2022-08-03-Innovations-relations.csv > /tmp/innovations-with-relations.csv
</span></span></code></pre></div><ul>
<li>Then I used SAFBuilder to create a SimpleItemArchive and import to DSpace Test:</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>$ export JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Dfile.encoding=UTF-8 -Xmx2048m"</span>
</span></span><span style="display:flex;"><span>$ dspace import --add --eperson<span style="color:#f92672">=</span>aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-08-03-innovations.map
</span></span></code></pre></div><ul>
<li>Meeting with Mohammed Salem about harmonizing MEL and CGSpace metadata fields
<ul>
<li>I still need to share our results and recommendations with Peter, Enrico, Sara, Svetlana, et al</li>
</ul>
</li>
<li>I made some minor fixes to csv-metadata-quality while working on the MARLO CRP Innovations</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/2022-08/">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>