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IWMI notified me that AReS was down with an HTTP 502 error
Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification
I don&rsquo;t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the angular_nginx container isn&rsquo;t running
I simply started it and AReS was running again:
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IWMI notified me that AReS was down with an HTTP 502 error
Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification
I don&rsquo;t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the angular_nginx container isn&rsquo;t running
I simply started it and AReS was running again:
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<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>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-06/">June, 2021</a></h2>
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<time datetime="2021-06-01T10:51:07+03:00">Tue Jun 01, 2021</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2021-06-01">2021-06-01</h2>
<ul>
<li>IWMI notified me that AReS was down with an HTTP 502 error
<ul>
<li>Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification</li>
<li>I don&rsquo;t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the <code>angular_nginx</code> container isn&rsquo;t running</li>
<li>I simply started it and AReS was running again:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ docker-compose -f docker/docker-compose.yml start angular_nginx
</code></pre><ul>
<li>Margarita from CCAFS emailed me to say that workflow alerts haven&rsquo;t been working lately
<ul>
<li>I guess this is related to the SMTP issues last week</li>
<li>I had fixed the config, but didn&rsquo;t restart Tomcat so DSpace didn&rsquo;t load the new variables</li>
<li>I ran all system updates on CGSpace (linode18) and DSpace Test (linode26) and rebooted the servers</li>
</ul>
</li>
</ul>
<h2 id="2021-06-03">2021-06-03</h2>
<ul>
<li>Meeting with AMCOW and IWMI to discuss AMCOW getting IWMI&rsquo;s content into the new AMCOW Knowledge Hub
<ul>
<li>At first we spent some time talking about DSpace communities/collections and the REST API, but then they said they actually prefer to send queries to sites on the fly and cache them in Redis for some time</li>
<li>That&rsquo;s when I thought they could perhaps use the OpenSearch, but I can&rsquo;t remember if it&rsquo;s possible to limit by community, or only collection&hellip;</li>
<li>Looking now, I see there is a &ldquo;scope&rdquo; parameter that can be used for community or collection, for example:</li>
</ul>
</li>
</ul>
<pre><code>https://cgspace.cgiar.org/open-search/discover?query=subject:water%20scarcity&amp;scope=10568/16814&amp;order=DESC&amp;rpp=100&amp;sort_by=2&amp;start=1
</code></pre><ul>
<li>That will sort by date issued (see: <code>webui.itemlist.sort-option.2</code> in dspace.cfg), give 100 results per page, and start on item 1</li>
<li>Otherwise, another alternative would be to use the IWMI CSV that we are already exporting every week</li>
<li>Fill out the <em>CGIAR-AGROVOC Task Group: Survey on the current CGIAR use of AGROVOC</em> survey on behalf of CGSpace</li>
</ul>
<h2 id="2021-06-06">2021-06-06</h2>
<ul>
<li>The Elasticsearch indexes are messed up so I dumped and re-created them correctly:</li>
</ul>
<pre><code class="language-console" data-lang="console">curl -XDELETE 'http://localhost:9200/openrxv-items-final'
curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
curl -XPUT 'http://localhost:9200/openrxv-items-final'
curl -XPUT 'http://localhost:9200/openrxv-items-temp'
curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{&quot;actions&quot; : [{&quot;add&quot; : { &quot;index&quot; : &quot;openrxv-items-final&quot;, &quot;alias&quot; : &quot;openrxv-items&quot;}}]}'
elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-final --type=data --limit=1000
</code></pre><ul>
<li>Then I started a harvesting on AReS</li>
</ul>
<h2 id="2021-06-07">2021-06-07</h2>
<ul>
<li>The harvesting on AReS completed successfully</li>
<li>Provide feedback to FAO on how we use AGROVOC for their &ldquo;AGROVOC call for use cases&rdquo;</li>
</ul>
<h2 id="2021-06-10">2021-06-10</h2>
<ul>
<li>Skype with Moayad to discuss AReS harvesting improvements
<ul>
<li>He will work on a plugin that reads the XML sitemap to get all item IDs and checks whether we have them or not</li>
</ul>
</li>
</ul>
<h2 id="2021-06-14">2021-06-14</h2>
<ul>
<li>Dump and re-create indexes on AReS (as above) so I can do a harvest</li>
</ul>
<h2 id="2021-06-16">2021-06-16</h2>
<ul>
<li>Looking at the Solr statistics on CGSpace for last month I see many requests from hosts using seemingly normal Windows browser user agents, but using the MSN bot&rsquo;s DNS
<ul>
<li>For example, user agent <code>Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.0; Trident/5.0; Trident/5.0)</code> with DNS <code>msnbot-131-253-25-91.search.msn.com.</code></li>
<li>I queried Solr for all hits using the MSN bot DNS (<code>dns:*msnbot* AND dns:*.msn.com.</code>) and found 457,706</li>
<li>I extracted their IPs using Solr&rsquo;s CSV format and ran them through my <code>resolve-addresses.py</code> script and found that they all belong to MICROSOFT-CORP-MSN-AS-BLOCK (AS8075)</li>
<li>Note that <a href="https://www.bing.com/webmasters/help/how-to-verify-bingbot-3905dc26">Microsoft&rsquo;s docs say that reverse lookups on Bingbot IPs will always have &ldquo;search.msn.com&rdquo;</a> so it is safe to purge these as non-human traffic</li>
<li>I purged the hits with <code>ilri/check-spider-ip-hits.sh</code> (though I had to do it in 3 batches because I forgot to increase the <code>facet.limit</code> so I was only getting them 100 at a time)</li>
</ul>
</li>
<li>Moayad sent a pull request a few days ago to re-work the harvesting on OpenRXV
<ul>
<li>It will hopefully also fix the duplicate and missing items issues</li>
<li>I had a Skype with him to discuss</li>
<li>I got it running on podman-compose, but I had to fix the storage permissions on the Elasticsearch volume after the first time it tries (and fails) to run:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ podman unshare chown 1000:1000 /home/aorth/.local/share/containers/storage/volumes/docker_esData_7/_data
</code></pre><ul>
<li>The new OpenRXV harvesting method by Moayad uses pages of 10 items instead of 100 and it&rsquo;s much faster
<ul>
<li>I harvested 90,000+ items from DSpace Test in ~3 hours</li>
<li>There seem to be some issues with the health check step though</li>
</ul>
</li>
</ul>
<h2 id="2021-06-17">2021-06-17</h2>
<ul>
<li>I ported my ilri/resolve-addresses.py script that uses IPAPI.co to use the local GeoIP2 databases
<ul>
<li>The new script is ilri/resolve-addresses-geoip2.py and it is much faster and works offline with no API rate limits</li>
</ul>
</li>
<li>Teams meeting with the CGIAR Metadata Working group to discuss CGSpace and open repositories and the way forward</li>
<li>More work with Moayad on OpenRXV harvesting issues
<ul>
<li>Using a JSON export from elasticdump we debugged the duplicate checker plugin and found that there are indeed duplicates:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ grep -oE '&quot;handle&quot;:&quot;[[:digit:]]+/[[:digit:]]+&quot;' openrxv-items_data.json | awk -F: '{print $2}' | wc -l
90459
$ grep -oE '&quot;handle&quot;:&quot;[[:digit:]]+/[[:digit:]]+&quot;' openrxv-items_data.json | awk -F: '{print $2}' | sort | uniq | wc -l
90380
$ grep -oE '&quot;handle&quot;:&quot;[[:digit:]]+/[[:digit:]]+&quot;' openrxv-items_data.json | awk -F: '{print $2}' | sort | uniq -c | sort -h
...
2 &quot;10568/99409&quot;
2 &quot;10568/99410&quot;
2 &quot;10568/99411&quot;
2 &quot;10568/99516&quot;
3 &quot;10568/102093&quot;
3 &quot;10568/103524&quot;
3 &quot;10568/106664&quot;
3 &quot;10568/106940&quot;
3 &quot;10568/107195&quot;
3 &quot;10568/96546&quot;
</code></pre><!-- raw HTML omitted -->
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-06/">June, 2021</a></li>
<li><a href="/cgspace-notes/2021-05/">May, 2021</a></li>
<li><a href="/cgspace-notes/2021-04/">April, 2021</a></li>
<li><a href="/cgspace-notes/2021-03/">March, 2021</a></li>
<li><a href="/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</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>
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