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Since yesterday there have been 10,000 REST errors and the site has been unstable again
I have blocked access to the API now
There are 3,000 IPs accessing the REST API in a 24-hour period!
# awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
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<meta name="twitter:description" content="2016-05-01
Since yesterday there have been 10,000 REST errors and the site has been unstable again
I have blocked access to the API now
There are 3,000 IPs accessing the REST API in a 24-hour period!
# awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
"/>
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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/2016-05/">May, 2016</a></h2>
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<time datetime="2016-05-01T23:06:00+03:00">Sun May 01, 2016</time>
in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
<li>I have blocked access to the API now</li>
<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
</ul>
<pre tabindex="0"><code># awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
</code></pre><ul>
<li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li>
<li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li>
</ul>
<pre tabindex="0"><code>GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1
</code></pre><ul>
<li>For now I&rsquo;ll block just the Ethiopian IP</li>
<li>The owner of that application has said that the <code>NaN</code> (not a number) is an error in his code and he&rsquo;ll fix it</li>
</ul>
<h2 id="2016-05-03">2016-05-03</h2>
<ul>
<li>Update nginx to 1.10.x branch on CGSpace</li>
<li>Fix a reference to <code>dc.type.output</code> in Discovery that I had missed when we migrated to <code>dc.type</code> last month (<a href="https://github.com/ilri/DSpace/pull/223">#223</a>)</li>
</ul>
<p><img src="/cgspace-notes/2016/05/discovery-types.png" alt="Item type in Discovery results"></p>
<h2 id="2016-05-06">2016-05-06</h2>
<ul>
<li>DSpace Test is down, <code>catalina.out</code> has lots of messages about heap space from some time yesterday (!)</li>
<li>It looks like Sisay was doing some batch imports</li>
<li>Hmm, also disk space is full</li>
<li>I decided to blow away the solr indexes, since they are 50GB and we don&rsquo;t really need all the Atmire stuff there right now</li>
<li>I will re-generate the Discovery indexes after re-deploying</li>
<li>Testing <code>renew-letsencrypt.sh</code> script for nginx</li>
</ul>
<pre tabindex="0"><code>#!/usr/bin/env bash
readonly SERVICE_BIN=/usr/sbin/service
readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto
# stop nginx so LE can listen on port 443
$SERVICE_BIN nginx stop
$LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 &gt; /var/log/letsencrypt/renew.log 2&gt;&amp;1
LE_RESULT=$?
$SERVICE_BIN nginx start
if [[ &#34;$LE_RESULT&#34; != 0 ]]; then
echo &#39;Automated renewal failed:&#39;
cat /var/log/letsencrypt/renew.log
exit 1
fi
</code></pre><ul>
<li>Seems to work well</li>
</ul>
<h2 id="2016-05-10">2016-05-10</h2>
<ul>
<li>Start looking at more metadata migrations</li>
<li>There are lots of fields in <code>dcterms</code> namespace that look interesting, like:
<ul>
<li>dcterms.type</li>
<li>dcterms.spatial</li>
</ul>
</li>
<li>Not sure what <code>dcterms</code> is&hellip;</li>
<li>Looks like these were <a href="https://wiki.lyrasis.org/display/DSDOC5x/Metadata+and+Bitstream+Format+Registries#MetadataandBitstreamFormatRegistries-DublinCoreTermsRegistry(DCTERMS)">added in DSpace 4</a> to allow for future work to make DSpace more flexible</li>
<li>CGSpace&rsquo;s <code>dc</code> registry has 96 items, and the default DSpace one has 73.</li>
</ul>
<h2 id="2016-05-11">2016-05-11</h2>
<ul>
<li>
<p>Identify and propose the next phase of CGSpace fields to migrate:</p>
<ul>
<li>dc.title.jtitle → cg.title.journal</li>
<li>dc.identifier.status → cg.identifier.status</li>
<li>dc.river.basin → cg.river.basin</li>
<li>dc.Species → cg.species</li>
<li>dc.targetaudience → cg.targetaudience</li>
<li>dc.fulltextstatus → cg.fulltextstatus</li>
<li>dc.editon → cg.edition</li>
<li>dc.isijournal → cg.isijournal</li>
</ul>
</li>
<li>
<p>Start a test rebase of the <code>5_x-prod</code> branch on top of the <code>dspace-5.5</code> tag</p>
</li>
<li>
<p>There were a handful of conflicts that I didn&rsquo;t understand</p>
</li>
<li>
<p>After completing the rebase I tried to build with the module versions Atmire had indicated as being 5.5 ready but I got this error:</p>
</li>
</ul>
<pre tabindex="0"><code>[ERROR] Failed to execute goal on project additions: Could not resolve dependencies for project org.dspace.modules:additions:jar:5.5: Could not find artifact com.atmire:atmire-metadata-quality-api:jar:5.5-2.10.1-0 in sonatype-releases (https://oss.sonatype.org/content/repositories/releases/) -&gt; [Help 1]
</code></pre><ul>
<li>I&rsquo;ve sent them a question about it</li>
<li>A user mentioned having problems with uploading a 33 MB PDF</li>
<li>I told her I would increase the limit temporarily tomorrow morning</li>
<li>Turns out she was able to decrease the size of the PDF so we didn&rsquo;t have to do anything</li>
</ul>
<h2 id="2016-05-12">2016-05-12</h2>
<ul>
<li>Looks like the issue that Abenet was having a few days ago with &ldquo;Connection Reset&rdquo; in Firefox might be due to a Firefox 46 issue: <a href="https://bugzilla.mozilla.org/show_bug.cgi?id=1268775">https://bugzilla.mozilla.org/show_bug.cgi?id=1268775</a></li>
<li>I finally found a copy of the latest CG Core metadata guidelines and it looks like we can add a few more fields to our next migration:
<ul>
<li>dc.rplace.region → cg.coverage.region</li>
<li>dc.cplace.country → cg.coverage.country</li>
</ul>
</li>
<li>Questions for CG people:
<ul>
<li>Our <code>dc.place</code> and <code>dc.srplace.subregion</code> could both map to <code>cg.coverage.admin-unit</code>?</li>
<li>Should we use <code>dc.contributor.crp</code> or <code>cg.contributor.crp</code> for the CRP (ours is <code>dc.crsubject.crpsubject</code>)?</li>
<li>Our <code>dc.contributor.affiliation</code> and <code>dc.contributor.corporate</code> could both map to <code>dc.contributor</code> and possibly <code>dc.contributor.center</code> depending on if it&rsquo;s a CG center or not</li>
<li><code>dc.title.jtitle</code> could either map to <code>dc.publisher</code> or <code>dc.source</code> depending on how you read things</li>
</ul>
</li>
<li>Found ~200 messed up CIAT values in <code>dc.publisher</code>:</li>
</ul>
<pre tabindex="0"><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to &#34;% %&#34;;
</code></pre><h2 id="2016-05-13">2016-05-13</h2>
<ul>
<li>More theorizing about CGcore</li>
<li>Add two new fields:
<ul>
<li>dc.srplace.subregion → cg.coverage.admin-unit</li>
<li>dc.place → cg.place</li>
</ul>
</li>
<li><code>dc.place</code> is our own field, so it&rsquo;s easy to move</li>
<li>I&rsquo;ve removed <code>dc.title.jtitle</code> from the list for now because there&rsquo;s no use moving it out of DC until we know where it will go (see discussion yesterday)</li>
</ul>
<h2 id="2016-05-18">2016-05-18</h2>
<ul>
<li>Work on 707 CCAFS records</li>
<li>They have thumbnails on Flickr and elsewhere</li>
<li>In OpenRefine I created a new <code>filename</code> column based on the <code>thumbnail</code> column with the following GREL:</li>
</ul>
<pre tabindex="0"><code>if(cells[&#39;thumbnails&#39;].value.contains(&#39;hqdefault&#39;), cells[&#39;thumbnails&#39;].value.split(&#39;/&#39;)[-2] + &#39;.jpg&#39;, cells[&#39;thumbnails&#39;].value.split(&#39;/&#39;)[-1])
</code></pre><ul>
<li>Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL</li>
<li>So for the <code>hqdefault.jpg</code> ones I just take the UUID (-2) and use it as the filename</li>
<li>Before importing with SAFBuilder I tested adding &ldquo;__bundle:THUMBNAIL&rdquo; to the <code>filename</code> column and it works fine</li>
</ul>
<h2 id="2016-05-19">2016-05-19</h2>
<ul>
<li>More quality control on <code>filename</code> field of CCAFS records to make processing in shell and SAFBuilder more reliable:</li>
</ul>
<pre tabindex="0"><code>value.replace(&#39;_&#39;,&#39;&#39;).replace(&#39;-&#39;,&#39;&#39;)
</code></pre><ul>
<li>We need to hold off on moving <code>dc.Species</code> to <code>cg.species</code> because it is only used for plants, and might be better to move it to something like <code>cg.species.plant</code></li>
<li>And <code>dc.identifier.fund</code> is MOSTLY used for CPWF project identifier but has some other sponsorship things
<ul>
<li>We should move PN*, SG*, CBA, IA, and PHASE* values to <code>cg.identifier.cpwfproject</code></li>
<li>The rest, like BMGF and USAID etc, might have to go to either <code>dc.description.sponsorship</code> or <code>cg.identifier.fund</code> (not sure yet)</li>
<li>There are also some mistakes in CPWF&rsquo;s things, like &ldquo;PN 47&rdquo;</li>
<li>This ought to catch all the CPWF values (there don&rsquo;t appear to be and SG* values):</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like &#39;PN%&#39; or text_value like &#39;PHASE%&#39; or text_value = &#39;CBA&#39; or text_value = &#39;IA&#39;);
</code></pre><h2 id="2016-05-20">2016-05-20</h2>
<ul>
<li>More work on CCAFS Video and Images records</li>
<li>For SAFBuilder we need to modify filename column to have the thumbnail bundle:</li>
</ul>
<pre tabindex="0"><code>value + &#34;__bundle:THUMBNAIL&#34;
</code></pre><ul>
<li>Also, I fixed some weird characters using OpenRefine&rsquo;s transform with the following GREL:</li>
</ul>
<pre tabindex="0"><code>value.replace(/\u0081/,&#39;&#39;)
</code></pre><ul>
<li>Write shell script to resize thumbnails with height larger than 400: <a href="https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256">https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256</a></li>
<li>Upload 707 CCAFS records to DSpace Test</li>
<li>A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target <code>_black</code>): <a href="https://github.com/ilri/DSpace/pull/224">#224</a></li>
<li>Work on configuration changes for Phase 2 metadata migrations</li>
</ul>
<h2 id="2016-05-23">2016-05-23</h2>
<ul>
<li>Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine</li>
<li>LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.</li>
<li>Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don&rsquo;t match!</li>
<li>I will have to try later</li>
</ul>
<h2 id="2016-05-30">2016-05-30</h2>
<ul>
<li>Export CCAFS video and image records from DSpace Test using the migrate option (<code>-m</code>):</li>
</ul>
<pre tabindex="0"><code>$ mkdir ~/ccafs-images
$ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m
</code></pre><ul>
<li>And then import to CGSpace:</li>
</ul>
<pre tabindex="0"><code>$ JAVA_OPTS=&#34;-Xmx512m -Dfile.encoding=UTF-8&#34; /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/70974 --source /tmp/ccafs-images --mapfile=/tmp/ccafs-images-may30.map &amp;&gt; /tmp/ccafs-images-may30.log
</code></pre><ul>
<li>But now we have double authors for &ldquo;CGIAR Research Program on Climate Change, Agriculture and Food Security&rdquo; in the authority</li>
<li>I&rsquo;m trying to do a Discovery index before messing with the authority index</li>
<li>Looks like we are missing the <code>index-authority</code> cron job, so who knows what&rsquo;s up with our authority index</li>
<li>Run system updates on DSpace Test, re-deploy code, and reboot the server</li>
<li>Clean up and import ~200 CTA records to CGSpace via CSV like:</li>
</ul>
<pre tabindex="0"><code>$ export JAVA_OPTS=&#34;-Xmx512m -Dfile.encoding=UTF-8&#34;
$ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &amp;&gt; ~/CTA-May30/CTA-42229.log
</code></pre><ul>
<li>Discovery indexing took a few hours for some reason, and after that I started the <code>index-authority</code> script</li>
</ul>
<pre tabindex="0"><code>$ JAVA_OPTS=&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34; /home/cgspace.cgiar.org/bin/dspace index-authority
</code></pre><h2 id="2016-05-31">2016-05-31</h2>
<ul>
<li>The <code>index-authority</code> script ran over night and was finished in the morning</li>
<li>Hopefully this was because we haven&rsquo;t been running it regularly and it will speed up next time</li>
<li>I am running it again with a timer to see:</li>
</ul>
<pre tabindex="0"><code>$ time /home/cgspace.cgiar.org/bin/dspace index-authority
Retrieving all data
Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
Cleaning the old index
Writing new data
All done !
real 37m26.538s
user 2m24.627s
sys 0m20.540s
</code></pre><ul>
<li>Update <code>tomcat7</code> crontab on CGSpace and DSpace Test to have the <code>index-authority</code> script that we were missing</li>
<li>Add new ILRI subject and CCAFS project tags to <code>input-forms.xml</code> (<a href="https://github.com/ilri/DSpace/pull/226">#226</a>, <a href="https://github.com/ilri/DSpace/pull/225">#225</a>)</li>
<li>Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.</li>
<li>Re-sync DSpace Test data with CGSpace</li>
<li>Clean up and import ~65 more CTA items into CGSpace</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
<li><a href="/cgspace-notes/2024-05/">May, 2024</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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