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<meta property="og:title" content="August, 2021" />
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<meta property="og:description" content="2021-08-01
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Update Docker images on AReS server (linode20) and reboot the server:
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# docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
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I decided to upgrade linode20 from Ubuntu 18.04 to 20.04
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-08/" />
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<meta property="article:published_time" content="2021-08-01T09:01:07+03:00" />
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<meta property="article:modified_time" content="2021-08-02T16:00:42+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="August, 2021"/>
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<meta name="twitter:description" content="2021-08-01
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Update Docker images on AReS server (linode20) and reboot the server:
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# docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
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I decided to upgrade linode20 from Ubuntu 18.04 to 20.04
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"/>
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<meta name="generator" content="Hugo 0.87.0" />
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"@type": "BlogPosting",
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"headline": "August, 2021",
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"url": "https://alanorth.github.io/cgspace-notes/2021-08/",
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"datePublished": "2021-08-01T09:01:07+03:00",
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"dateModified": "2021-08-02T16:00:42+03:00",
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2021-08/">
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<title>August, 2021 | CGSpace Notes</title>
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-08/">August, 2021</a></h2>
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<p class="blog-post-meta">
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<time datetime="2021-08-01T09:01:07+03:00">Sun Aug 01, 2021</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</header>
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<h2 id="2021-08-01">2021-08-01</h2>
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<ul>
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<li>Update Docker images on AReS server (linode20) and reboot the server:</li>
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</ul>
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<pre><code class="language-console" data-lang="console"># docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
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</code></pre><ul>
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<li>I decided to upgrade linode20 from Ubuntu 18.04 to 20.04</li>
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</ul>
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<ul>
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<li>First running all existing updates, taking some backups, checking for broken packages, and then rebooting:</li>
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</ul>
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<pre><code class="language-console" data-lang="console"># apt update && apt dist-upgrade
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# apt autoremove && apt autoclean
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# check for any packages with residual configs we can purge
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# dpkg -l | grep -E '^rc' | awk '{print $2}'
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# dpkg -l | grep -E '^rc' | awk '{print $2}' | xargs dpkg -P
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# dpkg -C
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# dpkg -l > 2021-08-01-linode20-dpkg.txt
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# tar -I zstd -cvf 2021-08-01-etc.tar.zst /etc
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# reboot
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# sed -i 's/bionic/focal/' /etc/apt/sources.list.d/*.list
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# do-release-upgrade
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</code></pre><ul>
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<li>… but of course it hit <a href="https://bugs.launchpad.net/ubuntu/+source/libxcrypt/+bug/1903838">the libxcrypt bug</a></li>
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<li>I had to get a copy of libcrypt.so.1.1.0 from a working Ubuntu 20.04 system and finish the upgrade manually</li>
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</ul>
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<pre><code class="language-console" data-lang="console"># apt install -f
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# apt dist-upgrade
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# reboot
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</code></pre><ul>
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<li>After rebooting I purged all packages with residual configs and cleaned up again:</li>
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</ul>
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<pre><code class="language-console" data-lang="console"># dpkg -l | grep -E '^rc' | awk '{print $2}' | xargs dpkg -P
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# apt autoremove && apt autoclean
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</code></pre><ul>
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<li>Then I cleared my local Ansible fact cache and re-ran the <a href="https://github.com/ilri/rmg-ansible-public">infrastructure playbooks</a></li>
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<li>Open <a href="https://github.com/ilri/OpenRXV/issues/111">an issue for the value mappings global replacement bug in OpenRXV</a></li>
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<li>Advise Peter and Abenet on expected CGSpace budget for 2022</li>
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<li>Start a fresh harvesting on AReS (linode20)</li>
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</ul>
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<h2 id="2021-08-02">2021-08-02</h2>
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<ul>
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<li>Help Udana with OAI validation on CGSpace
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<ul>
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<li>He was checking the OAI base URL on OpenArchives and I had to verify the results in order to proceed to Step 2</li>
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<li>Now it seems to be verified (all green): <a href="https://www.openarchives.org/Register/ValidateSite?log=R23ZWX85">https://www.openarchives.org/Register/ValidateSite?log=R23ZWX85</a></li>
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<li>We are listed in the OpenArchives list of databases conforming to OAI 2.0</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-08-03">2021-08-03</h2>
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<ul>
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<li>Run fresh re-harvest on AReS</li>
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</ul>
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<h2 id="2021-08-05">2021-08-05</h2>
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<ul>
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<li>Have a quick call with Mishell Portilla from CIP about a journal article that was flagged as being in a predatory journal (Beall’s List)
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<ul>
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<li>We agreed to unmap it from RTB’s collection for now, and I asked for advice from Peter and Abenet for what to do in the future</li>
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</ul>
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</li>
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<li>A developer from the Alliance asked for access to the CGSpace database so they can make some integration with PowerBI
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<ul>
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<li>I told them we don’t allow direct database access, and that it would be tricky anyways (that’s what APIs are for!)</li>
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</ul>
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</li>
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<li>I’m curious if there are still any requests coming in to CGSpace from the abusive Russian networks
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<ul>
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<li>I extracted all the unique IPs that nginx processed in the last week:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console"># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2 /var/log/nginx/access.log.3 /var/log/nginx/access.log.4 /var/log/nginx/access.log.5 /var/log/nginx/access.log.6 /var/log/nginx/access.log.7 /var/log/nginx/access.log.8 | grep -E " (200|499) " | grep -v -E "(mahider|Googlebot|Turnitin|Grammarly|Unpaywall|UptimeRobot|bot)" | awk '{print $1}' | sort | uniq > /tmp/2021-08-05-all-ips.txt
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# wc -l /tmp/2021-08-05-all-ips.txt
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43428 /tmp/2021-08-05-all-ips.txt
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</code></pre><ul>
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<li>Already I can see that the total is much less than during the attack on one weekend last month (over 50,000!)
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<ul>
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<li>Indeed, now I see that there are no IPs from those networks coming in now:</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ ./ilri/resolve-addresses-geoip2.py -i /tmp/2021-08-05-all-ips.txt -o /tmp/2021-08-05-all-ips.csv
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$ csvgrep -c asn -r '^(49453|46844|206485|62282|36352|35913|35624|8100)$' /tmp/2021-08-05-all-ips.csv | csvcut -c ip | sed 1d | sort | uniq > /tmp/2021-08-05-all-ips-to-purge.csv
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$ wc -l /tmp/2021-08-05-all-ips-to-purge.csv
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0 /tmp/2021-08-05-all-ips-to-purge.csv
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</code></pre><!-- raw HTML omitted -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2021-08/">August, 2021</a></li>
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<li><a href="/cgspace-notes/2021-07/">July, 2021</a></li>
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<li><a href="/cgspace-notes/2021-06/">June, 2021</a></li>
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<li><a href="/cgspace-notes/2021-05/">May, 2021</a></li>
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<li><a href="/cgspace-notes/2021-04/">April, 2021</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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