mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-22 21:22:19 +01:00
282 lines
8.1 KiB
HTML
282 lines
8.1 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="April, 2018" />
|
|
<meta property="og:description" content="2018-04-01
|
|
|
|
|
|
I tried to test something on DSpace Test but noticed that it’s down since god knows when
|
|
Catalina logs at least show some memory errors yesterday:
|
|
|
|
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-04/" />
|
|
|
|
|
|
|
|
<meta property="article:published_time" content="2018-04-01T16:13:54+02:00"/>
|
|
|
|
<meta property="article:modified_time" content="2018-04-04T15:57:34+03:00"/>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="April, 2018"/>
|
|
<meta name="twitter:description" content="2018-04-01
|
|
|
|
|
|
I tried to test something on DSpace Test but noticed that it’s down since god knows when
|
|
Catalina logs at least show some memory errors yesterday:
|
|
|
|
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.38" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "April, 2018",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2018-04/",
|
|
"wordCount": "423",
|
|
"datePublished": "2018-04-01T16:13:54+02:00",
|
|
"dateModified": "2018-04-04T15:57:34+03:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-04/">
|
|
|
|
<title>April, 2018 | CGSpace Notes</title>
|
|
|
|
<!-- combined, minified CSS -->
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-CoMzlF7G4xk3ftqRr7leobnWP85AuISUJljMFjtTG/UHyP/+bBwWAvBlXkB4VQQk" crossorigin="anonymous">
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</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"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
|
|
<p class="lead blog-description">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"><a href="https://alanorth.github.io/cgspace-notes/2018-04/">April, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-04-01T16:13:54+02:00">Sun Apr 01, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-04-01">2018-04-01</h2>
|
|
|
|
<ul>
|
|
<li>I tried to test something on DSpace Test but noticed that it’s down since god knows when</li>
|
|
<li>Catalina logs at least show some memory errors yesterday:</li>
|
|
</ul>
|
|
|
|
<p></p>
|
|
|
|
<pre><code>Mar 31, 2018 10:26:42 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
|
|
SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
|
|
java.lang.OutOfMemoryError: Java heap space
|
|
|
|
Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: Java heap space
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>So this is getting super annoying</li>
|
|
<li>I ran all system updates on DSpace Test and rebooted it</li>
|
|
<li>For some reason Listings and Reports is not giving any results for any queries now…</li>
|
|
<li>I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module</li>
|
|
<li>Help Lili Szilagyi with a question about statistics on some CCAFS items</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-04-04">2018-04-04</h2>
|
|
|
|
<ul>
|
|
<li>Peter noticed that there were still some old CRP names on CGSpace, because I hadn’t forced the Discovery index to be updated after I fixed the others last week</li>
|
|
<li>For completeness I re-ran the CRP corrections on CGSpace:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
|
|
Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Then started a full Discovery index:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
|
|
$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
|
|
|
real 76m13.841s
|
|
user 8m22.960s
|
|
sys 2m2.498s
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme’s items</li>
|
|
<li>I used my <a href="https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py">add-orcid-identifiers-csv.py</a> script:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>The CSV format of <code>jtohme-2018-04-04.csv</code> was:</li>
|
|
</ul>
|
|
|
|
<pre><code class="language-csv">dc.contributor.author,cg.creator.id
|
|
"Tohme, Joseph M.",Joe Tohme: 0000-0003-2765-7101
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>There was a quoting error in my CRP CSV and the replacements for <code>Forests, Trees and Agroforestry</code> got messed up</li>
|
|
<li>So I fixed them and had to re-index again!</li>
|
|
<li>I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ git checkout -b 5_x-dspace-5.8 5_x-prod
|
|
$ git reset --hard ilri/5_x-prod
|
|
$ git rebase -i dspace-5.8
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I was prepared to skip some commits that I had cherry picked from the upstream <code>dspace-5_x</code> branch when we did the DSpace 5.5 upgrade (see notes on 2016-10-19 and 2017-12-17):
|
|
|
|
<ul>
|
|
<li>[DS-3246] Improve cleanup in recyclable components (upstream commit on dspace-5_x: 9f0f5940e7921765c6a22e85337331656b18a403)</li>
|
|
<li>[DS-3250] applying patch provided by Atmire (upstream commit on dspace-5_x: c6fda557f731dbc200d7d58b8b61563f86fe6d06)</li>
|
|
<li>bump up to latest minor pdfbox version (upstream commit on dspace-5_x: b5330b78153b2052ed3dc2fd65917ccdbfcc0439)</li>
|
|
<li>DS-3583 Usage of correct Collection Array (#1731) (upstream commit on dspace-5_x: c8f62e6f496fa86846bfa6bcf2d16811087d9761)</li>
|
|
</ul></li>
|
|
<li>… but somehow git knew, and didn’t include them in my interactive rebase!</li>
|
|
<li>I need to send this branch to Atmire and also arrange payment (see <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">ticket #560</a> in their tracker)</li>
|
|
</ul>
|
|
|
|
|
|
|
|
|
|
|
|
</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/2018-04/">April, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2017-12/">December, 2017</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>
|
|
|
|
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>
|