mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-04 14:23:01 +01:00
508 lines
17 KiB
HTML
508 lines
17 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="CGSpace Notes" />
|
||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||
<meta property="og:type" content="website" />
|
||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
|
||
|
||
<meta property="og:updated_time" content="2019-03-01T12:16:30+01:00"/>
|
||
|
||
<meta name="twitter:card" content="summary"/>
|
||
<meta name="twitter:title" content="CGSpace Notes"/>
|
||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||
<meta name="generator" content="Hugo 0.54.0" />
|
||
|
||
|
||
|
||
<script type="application/ld+json">
|
||
{
|
||
"@context": "http://schema.org",
|
||
"@type": "Blog",
|
||
"headline": "CGSpace Notes",
|
||
"url" : "https://alanorth.github.io/cgspace-notes/",
|
||
"author": {
|
||
"@type": "Person",
|
||
"name": "Alan Orth"
|
||
},
|
||
"dateModified": "2019-03-01T12:16:30+01:00",
|
||
"keywords": "notes,notes,",
|
||
"description": "Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
|
||
}
|
||
</script>
|
||
|
||
|
||
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/">
|
||
|
||
<title>CGSpace Notes</title>
|
||
|
||
<!-- combined, minified CSS -->
|
||
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
|
||
|
||
|
||
<!-- RSS 2.0 feed -->
|
||
<link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+xml" title="CGSpace Notes" />
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</head>
|
||
|
||
<body>
|
||
|
||
|
||
<div class="blog-masthead">
|
||
<div class="container">
|
||
<nav class="nav blog-nav">
|
||
<a class="nav-link active" 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/2019-03/">March, 2019</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2019-03-01T12:16:30+01:00">Fri Mar 01, 2019</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="2019-03-01">2019-03-01</h2>
|
||
|
||
<ul>
|
||
<li>I checked IITA’s 259 Feb 14 records from last month for duplicates using Atmire’s Duplicate Checker on a fresh snapshot of CGSpace on my local machine and everything looks good</li>
|
||
<li>I am now only waiting to hear from her about where the items should go, though I assume Journal Articles go to IITA Journal Articles collection, etc…</li>
|
||
<li>Looking at the other half of Udana’s WLE records from 2018-11
|
||
|
||
<ul>
|
||
<li>I finished the ones for Restoring Degraded Landscapes (RDL), but these are for Variability, Risks and Competing Uses (VRC)</li>
|
||
<li>I did the usual cleanups for whitespace, added regions where they made sense for certain countries, cleaned up the DOI link formats, added rights information based on the publications page for a few items</li>
|
||
<li>Most worryingly, there are encoding errors in the abstracts for eleven items, for example:</li>
|
||
<li>68.15% <20> 9.45 instead of 68.15% ± 9.45</li>
|
||
<li>2003<EFBFBD>2013 instead of 2003–2013</li>
|
||
</ul></li>
|
||
<li>I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs</li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2019-03/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-02/">February, 2019</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2019-02-01T21:37:30+02:00">Fri Feb 01, 2019</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="2019-02-01">2019-02-01</h2>
|
||
|
||
<ul>
|
||
<li>Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!</li>
|
||
<li>The top IPs before, during, and after this latest alert tonight were:</li>
|
||
</ul>
|
||
|
||
<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "01/Feb/2019:(17|18|19|20|21)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
||
245 207.46.13.5
|
||
332 54.70.40.11
|
||
385 5.143.231.38
|
||
405 207.46.13.173
|
||
405 207.46.13.75
|
||
1117 66.249.66.219
|
||
1121 35.237.175.180
|
||
1546 5.9.6.51
|
||
2474 45.5.186.2
|
||
5490 85.25.237.71
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li><code>85.25.237.71</code> is the “Linguee Bot” that I first saw last month</li>
|
||
<li>The Solr statistics the past few months have been very high and I was wondering if the web server logs also showed an increase</li>
|
||
<li>There were just over 3 million accesses in the nginx logs last month:</li>
|
||
</ul>
|
||
|
||
<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2019"
|
||
3018243
|
||
|
||
real 0m19.873s
|
||
user 0m22.203s
|
||
sys 0m1.979s
|
||
</code></pre>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2019-02/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-01/">January, 2019</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2019-01-02T09:48:30+02:00">Wed Jan 02, 2019</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="2019-01-02">2019-01-02</h2>
|
||
|
||
<ul>
|
||
<li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li>
|
||
<li>I don’t see anything interesting in the web server logs around that time though:</li>
|
||
</ul>
|
||
|
||
<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
||
92 40.77.167.4
|
||
99 210.7.29.100
|
||
120 38.126.157.45
|
||
177 35.237.175.180
|
||
177 40.77.167.32
|
||
216 66.249.75.219
|
||
225 18.203.76.93
|
||
261 46.101.86.248
|
||
357 207.46.13.1
|
||
903 54.70.40.11
|
||
</code></pre>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2019-01/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-12/">December, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-12-02T02:09:30+02:00">Sun Dec 02, 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="2018-12-01">2018-12-01</h2>
|
||
|
||
<ul>
|
||
<li>Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK</li>
|
||
<li>I manually installed OpenJDK, then removed Oracle JDK, then re-ran the <a href="http://github.com/ilri/rmg-ansible-public">Ansible playbook</a> to update all configuration files, etc</li>
|
||
<li>Then I ran all system updates and restarted the server</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-12-02">2018-12-02</h2>
|
||
|
||
<ul>
|
||
<li>I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another <a href="https://usn.ubuntu.com/3831-1/">Ghostscript vulnerability last week</a></li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-12/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 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="2018-11-01">2018-11-01</h2>
|
||
|
||
<ul>
|
||
<li>Finalize AReS Phase I and Phase II ToRs</li>
|
||
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-11-03">2018-11-03</h2>
|
||
|
||
<ul>
|
||
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
|
||
<li>Today these are the top 10 IPs:</li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-11/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-10/">October, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-10-01T22:31:54+03:00">Mon Oct 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="2018-10-01">2018-10-01</h2>
|
||
|
||
<ul>
|
||
<li>Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items</li>
|
||
<li>I created a GitHub issue to track this <a href="https://github.com/ilri/DSpace/issues/389">#389</a>, because I’m super busy in Nairobi right now</li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-10/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-09/">September, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-09-02T09:55:54+03:00">Sun Sep 02, 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="2018-09-02">2018-09-02</h2>
|
||
|
||
<ul>
|
||
<li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li>
|
||
<li>I’ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
|
||
<li>Also, I’ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
|
||
<li>I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:</li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-09/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-08/">August, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 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="2018-08-01">2018-08-01</h2>
|
||
|
||
<ul>
|
||
<li>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</li>
|
||
</ul>
|
||
|
||
<pre><code>[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
|
||
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
|
||
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</li>
|
||
<li>From the DSpace log I see that eventually Solr stopped responding, so I guess the <code>java</code> process that was OOM killed above was Tomcat’s</li>
|
||
<li>I’m not sure why Tomcat didn’t crash with an OutOfMemoryError…</li>
|
||
<li>Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core</li>
|
||
<li>The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes</li>
|
||
<li>I ran all system updates on DSpace Test and rebooted it</li>
|
||
</ul>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-08/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-07-01T12:56:54+03:00">Sun Jul 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="2018-07-01">2018-07-01</h2>
|
||
|
||
<ul>
|
||
<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
|
||
</ul>
|
||
|
||
<pre><code>There is insufficient memory for the Java Runtime Environment to continue.
|
||
</code></pre>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-07/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
<article class="blog-post">
|
||
<header>
|
||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-06/">June, 2018</a></h2>
|
||
<p class="blog-post-meta"><time datetime="2018-06-04T19:49:54-07:00">Mon Jun 04, 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="2018-06-04">2018-06-04</h2>
|
||
|
||
<ul>
|
||
<li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>)
|
||
|
||
<ul>
|
||
<li>There seems to be a problem with the CUA and L&R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn’t build</li>
|
||
</ul></li>
|
||
<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
|
||
<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li>
|
||
<li>Time to index ~70,000 items on CGSpace:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
|
||
|
||
real 74m42.646s
|
||
user 8m5.056s
|
||
sys 2m7.289s
|
||
</code></pre>
|
||
<a href='https://alanorth.github.io/cgspace-notes/2018-06/'>Read more →</a>
|
||
</article>
|
||
|
||
|
||
|
||
|
||
|
||
<nav class="blog-pagination">
|
||
|
||
|
||
|
||
<a class="btn btn-outline-primary disabled" href="#" role="button" aria-disabled="true">Previous page</a>
|
||
<a class="btn btn-outline-primary" href="/cgspace-notes/page/2/" rel="next" role="button">Next page</a>
|
||
|
||
</nav>
|
||
|
||
|
||
|
||
|
||
|
||
</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/2019-03/">March, 2019</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2019-01/">January, 2019</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-12/">December, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-11/">November, 2018</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>
|