cgspace-notes/public/2017-11/index.html

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The CORE developers responded to say they are looking into their bot not respecting our robots.txt
2017-11-02
Today there have been no hits by CORE and no alerts from Linode (coincidence?)
# grep -c &quot;CORE&quot; /var/log/nginx/access.log
0
Generate list of authors on CGSpace for Peter to go through and correct:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
" />
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<meta name="twitter:description" content="2017-11-01
The CORE developers responded to say they are looking into their bot not respecting our robots.txt
2017-11-02
Today there have been no hits by CORE and no alerts from Linode (coincidence?)
# grep -c &quot;CORE&quot; /var/log/nginx/access.log
0
Generate list of authors on CGSpace for Peter to go through and correct:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
"/>
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<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>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54&#43;02:00">Thu Nov 02, 2017</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-11-01">2017-11-01</h2>
<ul>
<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
</ul>
<h2 id="2017-11-02">2017-11-02</h2>
<ul>
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
</ul>
<pre><code># grep -c &quot;CORE&quot; /var/log/nginx/access.log
0
</code></pre>
<ul>
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
</ul>
<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
</code></pre>
<p></p>
<ul>
<li>Abenet asked if it would be possible to generate a report of items in Listing and Reports that had &ldquo;International Fund for Agricultural Development&rdquo; as the <em>only</em> investor</li>
<li>I opened a ticket with Atmire to ask if this was possible: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=540">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=540</a></li>
<li>Work on making the thumbnails in the item view clickable</li>
<li>Basically, once you read the METS XML for an item it becomes easy to trace the structure to find the bitstream link</li>
</ul>
<pre><code>//mets:fileSec/mets:fileGrp[@USE='CONTENT']/mets:file/mets:FLocat[@LOCTYPE='URL']/@xlink:href
</code></pre>
<ul>
<li>METS XML is available for all items with this pattern: /metadata/handle/10568/95947/mets.xml</li>
<li>I whipped up a quick hack to print a clickable link with this URL on the thumbnail but it needs to check a few corner cases, like when there is a thumbnail but no content bitstream!</li>
<li>Help proof fifty-three CIAT records for Sisay: <a href="https://dspacetest.cgiar.org/handle/10568/95895">https://dspacetest.cgiar.org/handle/10568/95895</a></li>
<li>A handful of issues with <code>cg.place</code> using format like &ldquo;Lima, PE&rdquo; instead of &ldquo;Lima, Peru&rdquo;</li>
<li>Also, some dates like with completely invalid format like &ldquo;2010- 06&rdquo; and &ldquo;2011-3-28&rdquo;</li>
<li>I also collapsed some consecutive whitespace on a handful of fields</li>
</ul>
<h2 id="2017-11-03">2017-11-03</h2>
<ul>
<li>Atmire got back to us to say that they estimate it will take two days of labor to implement the change to Listings and Reports</li>
<li>I said I&rsquo;d ask Abenet if she wants that feature</li>
</ul>
<h2 id="2017-11-04">2017-11-04</h2>
<ul>
<li>I finished looking through Sisay&rsquo;s CIAT records for the &ldquo;Alianzas de Aprendizaje&rdquo; data</li>
<li>I corrected about half of the authors to standardize them</li>
<li>Linode emailed this morning to say that the CPU usage was high again, this time at 6:14AM</li>
<li>It&rsquo;s the first time in a few days that this has happened</li>
<li>I had a look to see what was going on, but it isn&rsquo;t the CORE bot:</li>
</ul>
<pre><code># awk '{print $1}' /var/log/nginx/access.log | sort -n | uniq -c | sort -h | tail
306 68.180.229.31
323 61.148.244.116
414 66.249.66.91
507 40.77.167.16
618 157.55.39.161
652 207.46.13.103
666 157.55.39.254
1173 104.196.152.243
1737 66.249.66.90
23101 138.201.52.218
</code></pre>
<ul>
<li>138.201.52.218 is from some Hetzner server, and I see it making 40,000 requests yesterday too, but none before that:</li>
</ul>
<pre><code># zgrep -c 138.201.52.218 /var/log/nginx/access.log*
/var/log/nginx/access.log:24403
/var/log/nginx/access.log.1:45958
/var/log/nginx/access.log.2.gz:0
/var/log/nginx/access.log.3.gz:0
/var/log/nginx/access.log.4.gz:0
/var/log/nginx/access.log.5.gz:0
/var/log/nginx/access.log.6.gz:0
</code></pre>
<ul>
<li>It&rsquo;s clearly a bot as it&rsquo;s making tens of thousands of requests, but it&rsquo;s using a &ldquo;normal&rdquo; user agent:</li>
</ul>
<pre><code>Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2227.0 Safari/537.36
</code></pre>
<ul>
<li>For now I don&rsquo;t know what this user is!</li>
</ul>
<h2 id="2017-11-05">2017-11-05</h2>
<ul>
<li>Peter asked if I could fix the appearance of &ldquo;International Livestock Research Institute&rdquo; in the author lookup during item submission</li>
<li>It looks to be just an issue with the user interface expecting authors to have both a first and last name:</li>
</ul>
<p><img src="/cgspace-notes/2017/11/author-lookup.png" alt="Author lookup" />
<img src="/cgspace-notes/2017/11/add-author.png" alt="Add author" /></p>
<ul>
<li>But in the database the authors are correct (none with weird <code>, /</code> characters):</li>
</ul>
<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue value where resource_type_id=2 and metadata_field_id=3 and text_value like 'International Livestock Research Institute%';
text_value | authority | confidence
--------------------------------------------+--------------------------------------+------------
International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | 0
International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc | 0
International Livestock Research Institute | | -1
International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | 600
International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc | -1
International Livestock Research Institute | | 600
International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | -1
International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | 500
(8 rows)
</code></pre>
<ul>
<li>So I&rsquo;m not sure if this is just a graphical glitch or if editors have to edit this metadata field prior to approval</li>
<li>Looking at monitoring Tomcat&rsquo;s JVM heap with Prometheus, it looks like we need to use JMX + <a href="https://github.com/prometheus/jmx_exporter">jmx_exporter</a></li>
<li>This guide shows how to <a href="https://geekflare.com/enable-jmx-tomcat-to-monitor-administer/">enable JMX in Tomcat</a> by modifying <code>CATALINA_OPTS</code></li>
<li>I was able to successfully connect to my local Tomcat with jconsole!</li>
</ul>
</article>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></li>
<li><a href="/cgspace-notes/2017-09/">September, 2017</a></li>
<li><a href="/cgspace-notes/2017-08/">August, 2017</a></li>
</ol>
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<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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