mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-18 19:22:18 +01:00
299 lines
9.7 KiB
HTML
299 lines
9.7 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="November, 2023" />
|
|
<meta property="og:description" content="2023-11-01
|
|
|
|
Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
|
|
|
|
I improved the filtering and wrote some Python using pandas to merge my sources more reliably
|
|
|
|
|
|
|
|
2023-11-02
|
|
|
|
Export CGSpace to check missing Initiative collection mappings
|
|
Start a harvest on AReS
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-11/" />
|
|
<meta property="article:published_time" content="2023-11-02T12:59:36+03:00" />
|
|
<meta property="article:modified_time" content="2023-11-02T20:58:43+03:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="November, 2023"/>
|
|
<meta name="twitter:description" content="2023-11-01
|
|
|
|
Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
|
|
|
|
I improved the filtering and wrote some Python using pandas to merge my sources more reliably
|
|
|
|
|
|
|
|
2023-11-02
|
|
|
|
Export CGSpace to check missing Initiative collection mappings
|
|
Start a harvest on AReS
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.120.3">
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "November, 2023",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2023-11/",
|
|
"wordCount": "487",
|
|
"datePublished": "2023-11-02T12:59:36+03:00",
|
|
"dateModified": "2023-11-02T20:58:43+03:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2023-11/">
|
|
|
|
<title>November, 2023 | 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/2023-11/">November, 2023</a></h2>
|
|
<p class="blog-post-meta">
|
|
<time datetime="2023-11-02T12:59:36+03:00">Thu Nov 02, 2023</time>
|
|
in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2023-11-01">2023-11-01</h2>
|
|
<ul>
|
|
<li>Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
|
|
<ul>
|
|
<li>I improved the filtering and wrote some Python using pandas to merge my sources more reliably</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-11-02">2023-11-02</h2>
|
|
<ul>
|
|
<li>Export CGSpace to check missing Initiative collection mappings</li>
|
|
<li>Start a harvest on AReS</li>
|
|
</ul>
|
|
<ul>
|
|
<li>IFPRI contacted us about importing their Slideshare presentations to CGSpace
|
|
<ul>
|
|
<li>There are ~1,700 of them and date back to as early as 2008</li>
|
|
<li>I did a quick cleanup of the metadata export from Slideshare (including tagging with some AGROVOC in OpenRefine) and uploaded to DSpace Test</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-11-03">2023-11-03</h2>
|
|
<ul>
|
|
<li>A little bit of work on the CGIAR Climate Change Synthesis</li>
|
|
<li>Discuss some CGSpace migration plans with Leigh from IFPRI
|
|
<ul>
|
|
<li>For their Slideshare content we agreed:
|
|
<ul>
|
|
<li>Exclude private</li>
|
|
<li>Exclude deleted</li>
|
|
<li>Exclude non presentation types</li>
|
|
<li>Exclude duplicates within the collection for now until we can sort them out</li>
|
|
</ul>
|
|
</li>
|
|
<li>That leaves about 1,500 items out of the 1,700</li>
|
|
</ul>
|
|
</li>
|
|
<li>I did a duplicate check against CGSpace and found 44 items with 1.0 similarity so I removed those</li>
|
|
</ul>
|
|
<h2 id="2023-11-04">2023-11-04</h2>
|
|
<ul>
|
|
<li>Export CGSpace to check for missing Initiative collection mappings</li>
|
|
<li>I ran through the list of potential duplicates on the IFPRI Slideshare presentations</li>
|
|
</ul>
|
|
<h2 id="2023-11-05">2023-11-05</h2>
|
|
<ul>
|
|
<li>Work with Salem to migrate AReS to the new version</li>
|
|
</ul>
|
|
<h2 id="2023-11-07">2023-11-07</h2>
|
|
<ul>
|
|
<li>DSpace 7 Test went down and there is very high load on the server
|
|
<ul>
|
|
<li>I saw very high load from Java but didn’t have time to check exactly what was wrong so I just rebooted the host</li>
|
|
<li>A few hours after restarting the system went down again, with very high load from Java again</li>
|
|
<li>I see lots of messages like this in the Tomcat log:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>tomcat9[732]: [9955.662s][info ][gc] GC(6291) Pause Full (G1 Compaction Pause) 4085M->4080M(4096M) 677.251ms
|
|
tomcat9[732]: [9955.662s][info ][gc] GC(6290) Concurrent Mark Cycle 677.558ms
|
|
tomcat9[732]: [9955.666s][info ][gc] GC(6292) To-space exhausted
|
|
</code></pre><ul>
|
|
<li>I see some messages in <code>dspace.log</code> about heap space:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>Caused by: java.lang.OutOfMemoryError: Java heap space
|
|
</code></pre><ul>
|
|
<li>I will increase Tomcat’s heap from 4096m to 5120m
|
|
<ul>
|
|
<li>A few hours later it happened again, so I increased the heap from 5120m to 6144m</li>
|
|
<li>Not sure what’s going on today…</li>
|
|
</ul>
|
|
</li>
|
|
<li>I tested moving the CGIAR Fund Council community to the CGIAR historic archive on 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>$ dspace community-filiator -r -p 10568/83389 -c 10947/2516
|
|
</span></span><span style="display:flex;"><span>$ dspace community-filiator -s -p 10947/2515 -c 10947/2516
|
|
</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10947/2516
|
|
</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10947/2515
|
|
</span></span><span style="display:flex;"><span>$ dspace index-discovery -r 10568/83389
|
|
</span></span><span style="display:flex;"><span>$ dspace index-discovery
|
|
</span></span></code></pre></div><ul>
|
|
<li>I think this is the minimal we can do to avoid a full Discovery reindex which is very expensive</li>
|
|
<li>I helped Maria resize some massive PDFs for upload to CGSpace using GhostScript prepress mode as I had done before in <a href="/cgspace-notes/2023-09/">September, 2023</a>,</li>
|
|
</ul>
|
|
<h2 id="2023-11-08">2023-11-08</h2>
|
|
<ul>
|
|
<li>DSpace 7 Test has very high load again and I see more Java heap space errors in the log</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># grep -c <span style="color:#e6db74">'Caused by: java.lang.OutOfMemoryError: Java heap space'</span> /home/dspace7/log/dspace.log-2023-11-07
|
|
</span></span><span style="display:flex;"><span>35
|
|
</span></span><span style="display:flex;"><span># grep -c <span style="color:#e6db74">'Caused by: java.lang.OutOfMemoryError: Java heap space'</span> /home/dspace7/log/dspace.log
|
|
</span></span><span style="display:flex;"><span>7
|
|
</span></span></code></pre></div><ul>
|
|
<li>I don’t know what is happening… I will increase the heap size from 6144m to 7168m again…</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/2023-11/">November, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-10/">October, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-09/">September, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-08/">August, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-07/">July, 2023</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>
|