mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-26 08:28:18 +01:00
302 lines
12 KiB
HTML
302 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="February, 2024" />
|
|
<meta property="og:description" content="2024-02-05
|
|
|
|
Delete duplicate metadata as described in my DSpace issue from last year: https://github.com/DSpace/DSpace/issues/8253
|
|
Lower case all the AGROVOC subjects on CGSpace
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-02/" />
|
|
<meta property="article:published_time" content="2024-02-05T11:10:00+03:00" />
|
|
<meta property="article:modified_time" content="2024-03-01T09:55:02+03:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="February, 2024"/>
|
|
<meta name="twitter:description" content="2024-02-05
|
|
|
|
Delete duplicate metadata as described in my DSpace issue from last year: https://github.com/DSpace/DSpace/issues/8253
|
|
Lower case all the AGROVOC subjects on CGSpace
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.131.0">
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "February, 2024",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2024-02/",
|
|
"wordCount": "560",
|
|
"datePublished": "2024-02-05T11:10:00+03:00",
|
|
"dateModified": "2024-03-01T09:55:02+03:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2024-02/">
|
|
|
|
<title>February, 2024 | CGSpace Notes</title>
|
|
|
|
|
|
<!-- combined, minified CSS -->
|
|
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F+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+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/2024-02/">February, 2024</a></h2>
|
|
<p class="blog-post-meta">
|
|
<time datetime="2024-02-05T11:10:00+03:00">Mon Feb 05, 2024</time>
|
|
in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2024-02-05">2024-02-05</h2>
|
|
<ul>
|
|
<li>Delete duplicate metadata as described in my DSpace issue from last year: <a href="https://github.com/DSpace/DSpace/issues/8253">https://github.com/DSpace/DSpace/issues/8253</a></li>
|
|
<li>Lower case all the AGROVOC subjects 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-sql" data-lang="sql"><span style="display:flex;"><span>dspace<span style="color:#f92672">=#</span> <span style="color:#66d9ef">BEGIN</span>;
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>
|
|
</span></span><span style="display:flex;"><span>dspace<span style="color:#f92672">=*#</span> <span style="color:#66d9ef">UPDATE</span> metadatavalue <span style="color:#66d9ef">SET</span> text_value<span style="color:#f92672">=</span><span style="color:#66d9ef">LOWER</span>(text_value) <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item) <span style="color:#66d9ef">AND</span> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">187</span> <span style="color:#66d9ef">AND</span> text_value <span style="color:#f92672">~</span> <span style="color:#e6db74">'[[:upper:]]'</span>;
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">UPDATE</span> <span style="color:#ae81ff">180</span>
|
|
</span></span><span style="display:flex;"><span>dspace<span style="color:#f92672">=*#</span> <span style="color:#66d9ef">COMMIT</span>;
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">COMMIT</span>
|
|
</span></span></code></pre></div><h2 id="2024-02-06">2024-02-06</h2>
|
|
<ul>
|
|
<li>Discuss IWMI using the CGSpace REST API for their new website</li>
|
|
<li>Export the IWMI community to extract their ORCID identifiers:</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>$ dspace metadata-export -i 10568/16814 -f /tmp/iwmi.csv
|
|
</span></span><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'cg.creator.identifier,cg.creator.identifier[en_US]'</span> ~/Downloads/2024-02-06-iwmi.csv <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' \
|
|
</span></span><span style="display:flex;"><span> | sort -u \
|
|
</span></span><span style="display:flex;"><span> | tee /tmp/iwmi-orcids.txt \
|
|
</span></span><span style="display:flex;"><span> | wc -l
|
|
</span></span><span style="display:flex;"><span>353
|
|
</span></span><span style="display:flex;"><span>$ ./ilri/resolve_orcids.py -i /tmp/iwmi-orcids.txt -o /tmp/iwmi-orcids-names.csv -d
|
|
</span></span></code></pre></div><ul>
|
|
<li>I noticed some similar looking names in our list so I clustered them in OpenRefine and manually checked a dozen or so to update our list</li>
|
|
</ul>
|
|
<h2 id="2024-02-07">2024-02-07</h2>
|
|
<ul>
|
|
<li>Maria asked me about the “missing” item from last week again
|
|
<ul>
|
|
<li>I can see it when I used the Admin search, but not in her workflow</li>
|
|
<li>It was submitted by TIP so I checked that user’s workspace and found it there</li>
|
|
<li>After depositing, it went into the workflow so Maria should be able to see it now</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-02-09">2024-02-09</h2>
|
|
<ul>
|
|
<li>Minor edits to CGSpace submission form</li>
|
|
<li>Upload 55 ISNAR book chapters to CGSpace from Peter</li>
|
|
</ul>
|
|
<h2 id="2024-02-19">2024-02-19</h2>
|
|
<ul>
|
|
<li>Looking into the collection mapping issue on CGSpace
|
|
<ul>
|
|
<li>It seems to be by design in DSpace 7: <a href="https://github.com/DSpace/dspace-angular/issues/1203">https://github.com/DSpace/dspace-angular/issues/1203</a></li>
|
|
<li>This is a massive setback for us…</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-02-20">2024-02-20</h2>
|
|
<ul>
|
|
<li>Minor work on OpenRXV to fix a bug in the ng-select drop downs</li>
|
|
<li>Minor work on the DSpace 7 nginx configuration to allow requesting robots.txt and sitemaps without hitting rate limits</li>
|
|
</ul>
|
|
<h2 id="2024-02-21">2024-02-21</h2>
|
|
<ul>
|
|
<li>Minor updates on OpenRXV, including one bug fix for missing mapped collections
|
|
<ul>
|
|
<li>Salem had to re-work the harvester for DSpace 7 since the mapped collections and parent collection list are separate!</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-02-22">2024-02-22</h2>
|
|
<ul>
|
|
<li>Discuss tagging of datasets and re-work the submission form to encourage use of DOI field for any item that has a DOI, and the normal URL field if not
|
|
<ul>
|
|
<li>The “cg.identifier.dataurl” field will be used for “related” datasets</li>
|
|
<li>I still have to check and move some metadata for existing datasets</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-02-23">2024-02-23</h2>
|
|
<ul>
|
|
<li>This morning Tomcat died due to an OOM kill from the kernel:</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>kernel: Out of memory: Killed process 698 (java) total-vm:14151300kB, anon-rss:9665812kB, file-rss:320kB, shmem-rss:0kB, UID:997 pgtables:20436kB oom_score_adj:0
|
|
</span></span></code></pre></div><ul>
|
|
<li>I don’t see any abnormal pattern in my Grafana graphs, for JVM or system load… very weird</li>
|
|
<li>I updated the submission form on CGSpace to include the new changes to URLs for datasets
|
|
<ul>
|
|
<li>I also updated about 80 datasets to move the URLs to the correct field</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2024-02-25">2024-02-25</h2>
|
|
<ul>
|
|
<li>This morning Tomcat died while I was doing a CSV export, with an OOM kill from the kernel:</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>kernel: Out of memory: Killed process 720768 (java) total-vm:14079976kB, anon-rss:9301684kB, file-rss:152kB, shmem-rss:0kB, UID:997 pgtables:19488kB oom_score_adj:0
|
|
</span></span></code></pre></div><ul>
|
|
<li>I don’t know why this is happening so often recently…</li>
|
|
</ul>
|
|
<h2 id="2024-02-27">2024-02-27</h2>
|
|
<ul>
|
|
<li>IFPRI sent me a list of authors to add to our list for now, until we can find a better way of doing it
|
|
<ul>
|
|
<li>I extracted the existing authors from our controlled vocabulary and combined them with IFPRI’s:</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-console" data-lang="console"><span style="display:flex;"><span>$ xmllint --xpath <span style="color:#e6db74">'//node/isComposedBy/node()'</span> dspace/config/controlled-vocabularies/dc-contributor-author.xml <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | grep -oE 'label=".*"' \
|
|
</span></span><span style="display:flex;"><span> | sed -e 's/label="//' -e 's/"$//' > /tmp/authors
|
|
</span></span><span style="display:flex;"><span>$ cat /tmp/authors /tmp/ifpri-authors | sort -u > /tmp/new-authors
|
|
</span></span></code></pre></div><h2 id="2024-02-28">2024-02-28</h2>
|
|
<ul>
|
|
<li>I figured out a way to add a new Angular component to handle all our relation fields</li>
|
|
</ul>
|
|
<h2 id="2024-02-29">2024-02-29</h2>
|
|
<ul>
|
|
<li>Clean up a bunch of metadata on CGSpace</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/2024-07/">July, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-03/">March, 2024</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>
|