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2019-04-01 16:02:54 +02:00
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Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
They asked if we had plans to enable RDF support in CGSpace
2019-05-05 15:45:12 +02:00
2019-04-01 16:02:54 +02:00
There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep &#39;Spore-192-EN-web.pdf&#39; | grep -E &#39;(18.196.196.108|18.195.78.144|18.195.218.6)&#39; | awk &#39;{print $9}&#39; | sort | uniq -c | sort -n | tail -n 5
2019-05-05 15:45:12 +02:00
4432 200
2019-04-01 16:02:54 +02:00
In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
2019-05-05 15:45:12 +02:00
Apply country and region corrections and deletions on DSpace Test and CGSpace:
2019-04-01 16:02:54 +02:00
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -f cg.coverage.country -m 228 -t ACTION -d
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p &#39;fuuu&#39; -f cg.coverage.region -m 231 -t action -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
2019-05-05 15:45:12 +02:00
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2019-08-08 17:10:44 +02:00
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2019-04-01 08:02:18 +02:00
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2019-04-01 16:02:54 +02:00
<meta name="twitter:description" content="2019-04-01
Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
They asked if we had plans to enable RDF support in CGSpace
2019-05-05 15:45:12 +02:00
2019-04-01 16:02:54 +02:00
There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep &#39;Spore-192-EN-web.pdf&#39; | grep -E &#39;(18.196.196.108|18.195.78.144|18.195.218.6)&#39; | awk &#39;{print $9}&#39; | sort | uniq -c | sort -n | tail -n 5
2019-05-05 15:45:12 +02:00
4432 200
2019-04-01 16:02:54 +02:00
In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
2019-05-05 15:45:12 +02:00
Apply country and region corrections and deletions on DSpace Test and CGSpace:
2019-04-01 16:02:54 +02:00
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -f cg.coverage.country -m 228 -t ACTION -d
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p &#39;fuuu&#39; -f cg.coverage.region -m 231 -t action -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
2019-05-05 15:45:12 +02:00
2019-04-01 16:02:54 +02:00
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2019-10-21 21:09:15 +02:00
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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>
2019-04-01 08:02:18 +02:00
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-04/">April, 2019</a></h2>
2019-04-01 08:02:18 +02:00
<p class="blog-post-meta"><time datetime="2019-04-01T09:00:43&#43;03:00">Mon Apr 01, 2019</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="2019-04-01">2019-04-01</h2>
2019-04-01 16:02:54 +02:00
<ul>
<li>Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
<ul>
<li>They asked if we had plans to enable RDF support in CGSpace</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today</p>
2019-04-01 16:02:54 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!</p>
2019-04-01 16:02:54 +02:00
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep 'Spore-192-EN-web.pdf' | grep -E '(18.196.196.108|18.195.78.144|18.195.218.6)' | awk '{print $9}' | sort | uniq -c | sort -n | tail -n 5
2019-05-05 15:45:12 +02:00
4432 200
</code></pre></li>
</ul></li>
2019-04-01 16:02:54 +02:00
2019-05-05 15:45:12 +02:00
<li><p>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</p></li>
<li><p>Apply country and region corrections and deletions on DSpace Test and CGSpace:</p>
2019-04-01 16:02:54 +02:00
<pre><code>$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.country -m 228 -t ACTION -d
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -m 231 -t action -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul>
2019-04-01 16:02:54 +02:00
2019-04-01 08:02:18 +02:00
<h2 id="2019-04-02">2019-04-02</h2>
2019-04-02 11:44:18 +02:00
<ul>
<li>CTA says the Amazon IPs are AWS gateways for real user traffic</li>
2019-04-02 19:32:18 +02:00
<li>I was trying to add Felix Shaw&rsquo;s account back to the Administrators group on DSpace Test, but I couldn&rsquo;t find his name in the user search of the groups page
<ul>
<li>If I searched for &ldquo;Felix&rdquo; or &ldquo;Shaw&rdquo; I saw other matches, included one for his personal email address!</li>
<li>I ended up finding him via searching for his email address</li>
</ul></li>
2019-04-02 11:44:18 +02:00
</ul>
2019-04-03 16:01:31 +02:00
<h2 id="2019-04-03">2019-04-03</h2>
<ul>
2019-05-05 15:45:12 +02:00
<li><p>Maria from Bioversity emailed me a list of new ORCID identifiers for their researchers so I will add them to our controlled vocabulary</p>
2019-04-03 16:01:31 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>First I need to extract the ones that are unique from their list compared to our existing one:</p>
2019-04-03 16:01:31 +02:00
2019-04-03 16:40:05 +02:00
<pre><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u &gt; /tmp/2019-04-03-orcid-ids.txt
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</code></pre></li>
</ul></li>
2019-04-03 16:01:31 +02:00
2019-05-05 15:45:12 +02:00
<li><p>We currently have 1177 unique ORCID identifiers, and this brings our total to 1237!</p></li>
<li><p>Next I will resolve all their names using my <code>resolve-orcids.py</code> script:</p>
2019-04-03 16:01:31 +02:00
<pre><code>$ ./resolve-orcids.py -i /tmp/2019-04-03-orcid-ids.txt -o 2019-04-03-orcid-ids.txt -d
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</code></pre></li>
2019-04-03 16:01:31 +02:00
2019-05-05 15:45:12 +02:00
<li><p>After that I added the XML formatting, formatted the file with tidy, and sorted the names in vim</p></li>
<li><p>One user&rsquo;s name has changed so I will update those using my <code>fix-metadata-values.py</code> script:</p>
2019-04-03 16:40:05 +02:00
<pre><code>$ ./fix-metadata-values.py -i 2019-04-03-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-03 16:40:05 +02:00
2019-07-04 18:37:10 +02:00
<li><p>I created a pull request and merged the changes to the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/417">#417</a>)</p></li>
2019-05-05 15:45:12 +02:00
<li><p>A few days ago I noticed some weird update process for the statistics-2018 Solr core and I see it&rsquo;s still going:</p>
2019-04-03 16:40:05 +02:00
<pre><code>2019-04-03 16:34:02,262 INFO org.dspace.statistics.SolrLogger @ Updating : 1754500/21701 docs in http://localhost:8081/solr//statistics-2018
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-03 16:40:05 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Interestingly, there are 5666 occurences, and they are mostly for the 2018 core:</p>
2019-04-03 16:40:05 +02:00
<pre><code>$ grep 'org.dspace.statistics.SolrLogger @ Updating' /home/cgspace.cgiar.org/log/dspace.log.2019-04-03 | awk '{print $11}' | sort | uniq -c
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1
3 http://localhost:8081/solr//statistics-2017
5662 http://localhost:8081/solr//statistics-2018
</code></pre></li>
2019-04-03 16:40:05 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I will have to keep an eye on it because nothing should be updating 2018 stats in 2019&hellip;</p></li>
2019-04-03 16:40:05 +02:00
</ul>
2019-04-05 21:22:41 +02:00
<h2 id="2019-04-05">2019-04-05</h2>
<ul>
<li>Uptime Robot reported that CGSpace (linode18) went down tonight</li>
2019-05-05 15:45:12 +02:00
<li><p>I see there are lots of PostgreSQL connections:</p>
2019-04-05 21:22:41 +02:00
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
2019-05-05 15:45:12 +02:00
5 dspaceApi
10 dspaceCli
250 dspaceWeb
</code></pre></li>
2019-04-05 21:22:41 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I still see those weird messages about updating the statistics-2018 Solr core:</p>
2019-04-05 21:22:41 +02:00
<pre><code>2019-04-05 21:06:53,770 INFO org.dspace.statistics.SolrLogger @ Updating : 2444600/21697 docs in http://localhost:8081/solr//statistics-2018
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-05 21:22:41 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Looking at <code>iostat 1 10</code> I also see some CPU steal has come back, and I can confirm it by looking at the Munin graphs:</p></li>
2019-04-05 21:22:41 +02:00
</ul>
<p><img src="/cgspace-notes/2019/04/cpu-week.png" alt="CPU usage week" /></p>
<ul>
<li>The other thing visible there is that the past few days the load has spiked to 500% and I don&rsquo;t think it&rsquo;s a coincidence that the Solr updating thing is happening&hellip;</li>
2019-05-05 15:45:12 +02:00
<li><p>I ran all system updates and rebooted the server</p>
2019-04-05 22:07:30 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>The load was lower on the server after reboot, but Solr didn&rsquo;t come back up properly according to the Solr Admin UI:</p>
2019-04-05 22:07:30 +02:00
<pre><code>statistics-2017: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-05 22:07:30 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I restarted it again and all the Solr cores came up properly&hellip;</p></li>
2019-04-05 21:22:41 +02:00
</ul>
2019-04-06 10:47:45 +02:00
<h2 id="2019-04-06">2019-04-06</h2>
<ul>
<li>Udana asked why item <a href="https://cgspace.cgiar.org/handle/10568/91278"><sup>10568</sup>&frasl;<sub>91278</sub></a> didn&rsquo;t have an Altmetric badge on CGSpace, but on the <a href="https://wle.cgiar.org/food-and-agricultural-innovation-pathways-prosperity">WLE website</a> it does
<ul>
<li>I looked and saw that the WLE website is using the Altmetric score associated with the DOI, and that the Handle has no score at all</li>
<li>I tweeted the item and I assume this will link the Handle with the DOI in the system</li>
2019-04-06 11:06:14 +02:00
<li>Twenty minutes later I see the same Altmetric score (9) on CGSpace</li>
2019-04-06 10:47:45 +02:00
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>Linode sent an alert that there was high CPU usage this morning on CGSpace (linode18) and these were the top IPs in the webserver access logs around the time:</p>
2019-04-06 10:47:45 +02:00
<pre><code># zcat --force /var/log/nginx/{access,error,library-access}.log /var/log/nginx/{access,error,library-access}.log.1 | grep -E &quot;06/Apr/2019:(06|07|08|09)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
222 18.195.78.144
245 207.46.13.58
303 207.46.13.194
328 66.249.79.33
564 207.46.13.210
566 66.249.79.62
575 40.77.167.66
1803 66.249.79.59
2834 2a01:4f8:140:3192::2
9623 45.5.184.72
2019-04-06 10:47:45 +02:00
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E &quot;06/Apr/2019:(06|07|08|09)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
31 66.249.79.62
41 207.46.13.210
42 40.77.167.66
54 42.113.50.219
132 66.249.79.59
785 2001:41d0:d:1990::
1164 45.5.184.72
2014 50.116.102.77
4267 45.5.186.2
4893 205.186.128.185
</code></pre></li>
<li><p><code>45.5.184.72</code> is in Colombia so it&rsquo;s probably CIAT, and I see they are indeed trying to get crawl the Discover pages on CIAT&rsquo;s datasets collection:</p>
2019-04-06 10:47:45 +02:00
<pre><code>GET /handle/10568/72970/discover?filtertype_0=type&amp;filtertype_1=author&amp;filter_relational_operator_1=contains&amp;filter_relational_operator_0=equals&amp;filter_1=&amp;filter_0=Dataset&amp;filtertype=dateIssued&amp;filter_relational_operator=equals&amp;filter=2014
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-06 10:47:45 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Their user agent is the one I added to the badbots list in nginx last week: &ldquo;GuzzleHttp/6.3.3 curl/7.47.0 PHP/7.0.30-0ubuntu0.16.04.1&rdquo;</p></li>
<li><p>They made 22,000 requests to Discover on this collection today alone (and it&rsquo;s only 11AM):</p>
2019-04-06 10:47:45 +02:00
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep &quot;06/Apr/2019&quot; | grep 45.5.184.72 | grep -oE '/handle/[0-9]+/[0-9]+/discover' | sort | uniq -c
2019-05-05 15:45:12 +02:00
22077 /handle/10568/72970/discover
</code></pre></li>
2019-04-06 10:47:45 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Yesterday they made 43,000 requests and we actually blocked most of them:</p>
2019-04-06 11:01:09 +02:00
<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep &quot;05/Apr/2019&quot; | grep 45.5.184.72 | grep -oE '/handle/[0-9]+/[0-9]+/discover' | sort | uniq -c
2019-05-05 15:45:12 +02:00
43631 /handle/10568/72970/discover
2019-04-06 11:01:09 +02:00
# zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep &quot;05/Apr/2019&quot; | grep 45.5.184.72 | grep -E '/handle/[0-9]+/[0-9]+/discover' | awk '{print $9}' | sort | uniq -c
2019-05-05 15:45:12 +02:00
142 200
43489 503
</code></pre></li>
2019-04-06 11:01:09 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I need to find a contact at CIAT to tell them to use the REST API rather than crawling Discover</p></li>
<li><p>Maria from Bioversity recommended that we use the phrase &ldquo;AGROVOC subject&rdquo; instead of &ldquo;Subject&rdquo; in Listings and Reports</p>
2019-04-06 10:47:45 +02:00
<ul>
<li>I made a pull request to update this and merged it to the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/418">#418</a>)</li>
</ul></li>
</ul>
2019-04-07 10:45:34 +02:00
<h2 id="2019-04-07">2019-04-07</h2>
<ul>
<li>Looking into the impact of harvesters like <code>45.5.184.72</code>, I see in Solr that this user is not categorized as a bot so it definitely impacts the usage stats by some tens of thousands <em>per day</em></li>
2019-05-05 15:45:12 +02:00
<li><p>Last week CTA switched their frontend code to use HEAD requests instead of GET requests for bitstreams</p>
2019-04-07 10:45:34 +02:00
<ul>
<li>I am trying to see if these are registered as downloads in Solr or not</li>
2019-05-05 15:45:12 +02:00
<li><p>I see 96,925 downloads from their AWS gateway IPs in 2019-03:</p>
2019-04-07 10:45:34 +02:00
<pre><code>$ http --print b 'http://localhost:8081/solr/statistics/select?q=type%3A0+AND+(ip%3A18.196.196.108+OR+ip%3A18.195.78.144+OR+ip%3A18.195.218.6)&amp;fq=statistics_type%3Aview&amp;fq=bundleName%3AORIGINAL&amp;fq=dateYearMonth%3A2019-03&amp;rows=0&amp;wt=json&amp;indent=true'
{
2019-05-05 15:45:12 +02:00
&quot;response&quot;: {
&quot;docs&quot;: [],
&quot;numFound&quot;: 96925,
&quot;start&quot;: 0
},
&quot;responseHeader&quot;: {
&quot;QTime&quot;: 1,
&quot;params&quot;: {
&quot;fq&quot;: [
&quot;statistics_type:view&quot;,
&quot;bundleName:ORIGINAL&quot;,
&quot;dateYearMonth:2019-03&quot;
],
&quot;indent&quot;: &quot;true&quot;,
&quot;q&quot;: &quot;type:0 AND (ip:18.196.196.108 OR ip:18.195.78.144 OR ip:18.195.218.6)&quot;,
&quot;rows&quot;: &quot;0&quot;,
&quot;wt&quot;: &quot;json&quot;
},
&quot;status&quot;: 0
2019-04-07 10:45:34 +02:00
}
2019-05-05 15:45:12 +02:00
}
</code></pre></li>
</ul></li>
2019-04-07 10:45:34 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Strangely I don&rsquo;t see many hits in 2019-04:</p>
2019-04-07 10:45:34 +02:00
<pre><code>$ http --print b 'http://localhost:8081/solr/statistics/select?q=type%3A0+AND+(ip%3A18.196.196.108+OR+ip%3A18.195.78.144+OR+ip%3A18.195.218.6)&amp;fq=statistics_type%3Aview&amp;fq=bundleName%3AORIGINAL&amp;fq=dateYearMonth%3A2019-04&amp;rows=0&amp;wt=json&amp;indent=true'
{
2019-05-05 15:45:12 +02:00
&quot;response&quot;: {
&quot;docs&quot;: [],
&quot;numFound&quot;: 38,
&quot;start&quot;: 0
},
&quot;responseHeader&quot;: {
&quot;QTime&quot;: 1,
&quot;params&quot;: {
&quot;fq&quot;: [
&quot;statistics_type:view&quot;,
&quot;bundleName:ORIGINAL&quot;,
&quot;dateYearMonth:2019-04&quot;
],
&quot;indent&quot;: &quot;true&quot;,
&quot;q&quot;: &quot;type:0 AND (ip:18.196.196.108 OR ip:18.195.78.144 OR ip:18.195.218.6)&quot;,
&quot;rows&quot;: &quot;0&quot;,
&quot;wt&quot;: &quot;json&quot;
2019-04-07 10:45:34 +02:00
},
2019-05-05 15:45:12 +02:00
&quot;status&quot;: 0
}
2019-04-07 10:45:34 +02:00
}
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-07 10:45:34 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Making some tests on GET vs HEAD requests on the <a href="https://dspacetest.cgiar.org/handle/10568/100289">CTA Spore 192 item</a> on DSpace Test:</p>
2019-04-07 10:45:34 +02:00
<pre><code>$ http --print Hh GET https://dspacetest.cgiar.org/bitstream/handle/10568/100289/Spore-192-EN-web.pdf
GET /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: dspacetest.cgiar.org
User-Agent: HTTPie/1.0.2
HTTP/1.1 200 OK
Connection: keep-alive
Content-Language: en-US
Content-Length: 2069158
Content-Type: application/pdf;charset=ISO-8859-1
Date: Sun, 07 Apr 2019 08:38:34 GMT
Expires: Sun, 07 Apr 2019 09:38:34 GMT
Last-Modified: Thu, 14 Mar 2019 11:20:05 GMT
Server: nginx
Set-Cookie: JSESSIONID=21A492CC31CA8845278DFA078BD2D9ED; Path=/; Secure; HttpOnly
Vary: User-Agent
X-Cocoon-Version: 2.2.0
X-Content-Type-Options: nosniff
X-Frame-Options: SAMEORIGIN
X-Robots-Tag: none
X-XSS-Protection: 1; mode=block
$ http --print Hh HEAD https://dspacetest.cgiar.org/bitstream/handle/10568/100289/Spore-192-EN-web.pdf
HEAD /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: dspacetest.cgiar.org
User-Agent: HTTPie/1.0.2
HTTP/1.1 200 OK
Connection: keep-alive
Content-Language: en-US
Content-Length: 2069158
Content-Type: application/pdf;charset=ISO-8859-1
Date: Sun, 07 Apr 2019 08:39:01 GMT
Expires: Sun, 07 Apr 2019 09:39:01 GMT
Last-Modified: Thu, 14 Mar 2019 11:20:05 GMT
Server: nginx
Set-Cookie: JSESSIONID=36C8502257CC6C72FD3BC9EBF91C4A0E; Path=/; Secure; HttpOnly
Vary: User-Agent
X-Cocoon-Version: 2.2.0
X-Content-Type-Options: nosniff
X-Frame-Options: SAMEORIGIN
X-Robots-Tag: none
X-XSS-Protection: 1; mode=block
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-07 10:45:34 +02:00
2019-05-05 15:45:12 +02:00
<li><p>And from the server side, the nginx logs show:</p>
2019-04-07 10:45:34 +02:00
<pre><code>78.x.x.x - - [07/Apr/2019:01:38:35 -0700] &quot;GET /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1&quot; 200 68078 &quot;-&quot; &quot;HTTPie/1.0.2&quot;
78.x.x.x - - [07/Apr/2019:01:39:01 -0700] &quot;HEAD /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1&quot; 200 0 &quot;-&quot; &quot;HTTPie/1.0.2&quot;
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-07 10:45:34 +02:00
2019-05-05 15:45:12 +02:00
<li><p>So definitely the <em>size</em> of the transfer is more efficient with a HEAD, but I need to wait to see if these requests show up in Solr</p>
2019-04-07 17:08:38 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>After twenty minutes of waiting I still don&rsquo;t see any new requests in the statistics core, but when I try the requests from the command line again I see the following in the DSpace log:</p>
2019-04-07 17:08:38 +02:00
<pre><code>2019-04-07 02:05:30,966 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous:session_id=EF2DB6E4F69926C5555B3492BB0071A8:ip_addr=78.x.x.x:view_bitstream:bitstream_id=165818
2019-04-07 02:05:39,265 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous:session_id=B6381FC590A5160D84930102D068C7A3:ip_addr=78.x.x.x:view_bitstream:bitstream_id=165818
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-07 17:08:38 +02:00
2019-05-05 15:45:12 +02:00
<li><p>So my inclination is that both HEAD and GET requests are registered as views as far as Solr and DSpace are concerned</p>
2019-04-07 17:08:38 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>Strangely, the statistics Solr core says it hasn&rsquo;t been modified in 24 hours, so I tried to start the &ldquo;optimize&rdquo; process from the Admin UI and I see this in the Solr log:</p>
2019-04-07 17:08:38 +02:00
<pre><code>2019-04-07 02:08:44,186 INFO org.apache.solr.update.UpdateHandler @ start commit{,optimize=true,openSearcher=true,waitSearcher=true,expungeDeletes=false,softCommit=false,prepareCommit=false}
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-07 17:08:38 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Ugh, even after optimizing there are no Solr results for requests from my IP, and actually I only see 18 results from 2019-04 so far and none of them are <code>statistics_type:view</code>&hellip; very weird</p>
2019-04-07 17:08:38 +02:00
<ul>
<li>I don&rsquo;t even see many hits for days after 2019-03-17, when I migrated the server to Ubuntu 18.04 and copied the statistics core from CGSpace (linode18)</li>
<li>I will try to re-deploy the <code>5_x-dev</code> branch and test again</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>According to the <a href="https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics">DSpace 5.x Solr documentation</a> the default commit time is after 15 minutes or 10,000 documents (see <code>solrconfig.xml</code>)</p></li>
<li><p>I looped some GET and HEAD requests to a bitstream on my local instance and after some time I see that they <em>do</em> register as downloads (even though they are internal):</p>
2019-04-07 17:08:38 +02:00
<pre><code>$ http --print b 'http://localhost:8080/solr/statistics/select?q=type%3A0+AND+time%3A2019-04-07*&amp;fq=statistics_type%3Aview&amp;fq=isInternal%3Atrue&amp;rows=0&amp;wt=json&amp;indent=true'
{
2019-05-05 15:45:12 +02:00
&quot;response&quot;: {
&quot;docs&quot;: [],
&quot;numFound&quot;: 909,
&quot;start&quot;: 0
},
&quot;responseHeader&quot;: {
&quot;QTime&quot;: 0,
&quot;params&quot;: {
&quot;fq&quot;: [
&quot;statistics_type:view&quot;,
&quot;isInternal:true&quot;
],
&quot;indent&quot;: &quot;true&quot;,
&quot;q&quot;: &quot;type:0 AND time:2019-04-07*&quot;,
&quot;rows&quot;: &quot;0&quot;,
&quot;wt&quot;: &quot;json&quot;
2019-04-07 17:08:38 +02:00
},
2019-05-05 15:45:12 +02:00
&quot;status&quot;: 0
2019-04-07 17:08:38 +02:00
}
2019-05-05 15:45:12 +02:00
}
</code></pre></li>
2019-04-07 17:08:38 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I confirmed the same on CGSpace itself after making one HEAD request</p></li>
<li><p>So I&rsquo;m pretty sure it&rsquo;s something about DSpace Test using the CGSpace statistics core, and not that I deployed Solr 4.10.4 there last week</p>
2019-04-07 17:08:38 +02:00
<ul>
<li>I deployed Solr 4.10.4 locally and ran a bunch of requests for bitstreams and they do show up in the Solr statistics log, so the issue must be with re-using the existing Solr core from CGSpace</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>Now this gets more frustrating: I did the same GET and HEAD tests on a local Ubuntu 16.04 VM with Solr 4.10.2 and 4.10.4 and the statistics are recorded</p>
2019-04-07 17:08:38 +02:00
<ul>
<li>This leads me to believe there is something specifically wrong with DSpace Test (linode19)</li>
<li>The only thing I can think of is that the JVM is using G1GC instead of ConcMarkSweepGC</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>Holy shit, all this is actually because of the GeoIP1 deprecation and a missing <code>GeoLiteCity.dat</code></p>
2019-04-07 17:08:38 +02:00
<ul>
<li>For some reason the missing GeoIP data causes stats to not be recorded whatsoever and there is no error!</li>
<li>See: <a href="https://jira.duraspace.org/browse/DS-3986">DS-3986</a></li>
<li>See: <a href="https://jira.duraspace.org/browse/DS-4020">DS-4020</a></li>
<li>See: <a href="https://jira.duraspace.org/browse/DS-3832">DS-3832</a></li>
<li>DSpace 5.10 upgraded to use GeoIP2, but we are on 5.8 so I just copied the missing database file from another server because it has been <em>removed</em> from MaxMind&rsquo;s server as of 2018-04-01</li>
<li>Now I made 100 requests and I see them in the Solr statistics&hellip; fuck my life for wasting five hours debugging this</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>UptimeRobot said CGSpace went down and up a few times tonight, and my first instict was to check <code>iostat 1 10</code> and I saw that CPU steal is around 1030 percent right now&hellip;</p></li>
<li><p>The load average is super high right now, as I&rsquo;ve noticed the last few times UptimeRobot said that CGSpace went down:</p>
2019-04-07 20:05:52 +02:00
<pre><code>$ cat /proc/loadavg
10.70 9.17 8.85 18/633 4198
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-07 20:05:52 +02:00
2019-05-05 15:45:12 +02:00
<li><p>According to the server logs there is actually not much going on right now:</p>
2019-04-07 20:05:52 +02:00
2019-04-07 20:17:16 +02:00
<pre><code># zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E &quot;07/Apr/2019:(18|19|20)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
118 18.195.78.144
128 207.46.13.219
129 167.114.64.100
159 207.46.13.129
179 207.46.13.33
188 2408:8214:7a00:868f:7c1e:e0f3:20c6:c142
195 66.249.79.59
363 40.77.167.21
740 2a01:4f8:140:3192::2
4823 45.5.184.72
2019-04-07 20:17:16 +02:00
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E &quot;07/Apr/2019:(18|19|20)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
3 66.249.79.62
3 66.249.83.196
4 207.46.13.86
5 82.145.222.150
6 2a01:4f9:2b:1263::2
6 41.204.190.40
7 35.174.176.49
10 40.77.167.21
11 194.246.119.6
11 66.249.79.59
</code></pre></li>
<li><p><code>45.5.184.72</code> is CIAT, who I already blocked and am waiting to hear from</p></li>
<li><p><code>2a01:4f8:140:3192::2</code> is BLEXbot, which should be handled by the Tomcat Crawler Session Manager Valve</p></li>
<li><p><code>2408:8214:7a00:868f:7c1e:e0f3:20c6:c142</code> is some stupid Chinese bot making malicious POST requests</p></li>
<li><p>There are free database connections in the pool:</p>
2019-04-07 20:15:03 +02:00
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
2019-05-05 15:45:12 +02:00
5 dspaceApi
7 dspaceCli
23 dspaceWeb
</code></pre></li>
2019-04-07 20:15:03 +02:00
2019-05-05 15:45:12 +02:00
<li><p>It seems that the issue with CGSpace being &ldquo;down&rdquo; is actually because of CPU steal again!!!</p></li>
<li><p>I opened a ticket with support and asked them to migrate the VM to a less busy host</p></li>
2019-04-07 10:45:34 +02:00
</ul>
2019-04-08 10:26:20 +02:00
<h2 id="2019-04-08">2019-04-08</h2>
<ul>
2019-05-05 15:45:12 +02:00
<li><p>Start checking IITA&rsquo;s last round of batch uploads from <a href="https://dspacetest.cgiar.org/handle/10568/100333">March on DSpace Test</a> (20193rd.xls)</p>
2019-04-08 10:26:20 +02:00
<ul>
<li>Lots of problems with affiliations, I had to correct about sixty of them</li>
2019-05-05 15:45:12 +02:00
<li><p>I used lein to host the latest CSV of our affiliations for OpenRefine to reconcile against:</p>
2019-04-08 10:26:20 +02:00
<pre><code>$ lein run ~/src/git/DSpace/2019-02-22-affiliations.csv name id
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-08 10:26:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>After matching the values and creating some new matches I had trouble remembering how to copy the reconciled values to a new column</p>
2019-04-08 10:26:20 +02:00
<ul>
<li>The matched values can be accessed with <code>cell.recon.match.name</code>, but some of the new values don&rsquo;t appear, perhaps because I edited the original cell values?</li>
2019-05-05 15:45:12 +02:00
<li><p>I ended up using this GREL expression to copy all values to a new column:</p>
2019-04-08 10:26:20 +02:00
<pre><code>if(cell.recon.matched, cell.recon.match.name, value)
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-08 10:26:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>See the <a href="https://github.com/OpenRefine/OpenRefine/wiki/Variables#recon">OpenRefine variables documentation</a> for more notes about the <code>recon</code> object</p></li>
<li><p>I also noticed a handful of errors in our current list of affiliations so I corrected them:</p>
2019-04-08 10:26:20 +02:00
<pre><code>$ ./fix-metadata-values.py -i 2019-04-08-fix-13-affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211 -t correct -d
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-08 10:26:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>We should create a new list of affiliations to update our controlled vocabulary again</p></li>
<li><p>I dumped a list of the top 1500 affiliations:</p>
2019-04-08 10:26:20 +02:00
2019-04-08 15:29:20 +02:00
<pre><code>dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 211 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2019-04-08-top-1500-affiliations.csv WITH CSV HEADER;
COPY 1500
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-08 15:29:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Fix a few more messed up affiliations that have return characters in them (use Ctrl-V Ctrl-M to re-create control character):</p>
2019-04-08 15:29:20 +02:00
<pre><code>dspace=# UPDATE metadatavalue SET text_value='International Institute for Environment and Development' WHERE resource_type_id = 2 AND metadata_field_id = 211 AND text_value LIKE 'International Institute^M%';
dspace=# UPDATE metadatavalue SET text_value='Kenya Agriculture and Livestock Research Organization' WHERE resource_type_id = 2 AND metadata_field_id = 211 AND text_value LIKE 'Kenya Agricultural and Livestock Research^M%';
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-08 15:29:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I noticed a bunch of subjects and affiliations that use stylized apostrophes so I will export those and then batch update them:</p>
2019-04-08 15:29:20 +02:00
<pre><code>dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 AND text_value LIKE '%%') to /tmp/2019-04-08-affiliations-apostrophes.csv WITH CSV HEADER;
COPY 60
dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 57 AND text_value LIKE '%%') to /tmp/2019-04-08-subject-apostrophes.csv WITH CSV HEADER;
COPY 20
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-08 15:29:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I cleaned them up in OpenRefine and then applied the fixes on CGSpace and DSpace Test:</p>
2019-04-08 15:29:20 +02:00
<pre><code>$ ./fix-metadata-values.py -i /tmp/2019-04-08-fix-60-affiliations-apostrophes.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211 -t correct -d
$ ./fix-metadata-values.py -i /tmp/2019-04-08-fix-20-subject-apostrophes.csv -db dspace -u dspace -p 'fuuu' -f dc.subject -m 57 -t correct -d
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-08 15:29:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>UptimeRobot said that CGSpace (linode18) went down tonight</p>
2019-04-08 18:55:20 +02:00
<ul>
<li>The load average is at <code>9.42, 8.87, 7.87</code></li>
2019-05-05 15:45:12 +02:00
<li><p>I looked at PostgreSQL and see shitloads of connections there:</p>
2019-04-08 18:55:20 +02:00
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
2019-05-05 15:45:12 +02:00
5 dspaceApi
7 dspaceCli
250 dspaceWeb
</code></pre></li>
</ul></li>
2019-04-08 18:55:20 +02:00
2019-05-05 15:45:12 +02:00
<li><p>On a related note I see connection pool errors in the DSpace log:</p>
2019-04-08 19:03:58 +02:00
<pre><code>2019-04-08 19:01:10,472 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-319] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:250; idle:0; lastwait:5000].
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-08 19:03:58 +02:00
2019-05-05 15:45:12 +02:00
<li><p>But still I see 10 to 30% CPU steal in <code>iostat</code> that is also reflected in the Munin graphs:</p></li>
2019-04-08 19:22:40 +02:00
</ul>
<p><img src="/cgspace-notes/2019/04/cpu-week2.png" alt="CPU usage week" /></p>
<ul>
2019-04-08 18:55:20 +02:00
<li>Linode Support still didn&rsquo;t respond to my ticket from yesterday, so I attached a new output of <code>iostat 1 10</code> and asked them to move the VM to a less busy host</li>
2019-05-05 15:45:12 +02:00
<li><p>The web server logs are not very busy:</p>
2019-04-08 19:00:45 +02:00
<pre><code># zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E &quot;08/Apr/2019:(17|18|19)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
124 40.77.167.135
135 95.108.181.88
139 157.55.39.206
190 66.249.79.133
202 45.5.186.2
284 207.46.13.95
359 18.196.196.108
457 157.55.39.164
457 40.77.167.132
3822 45.5.184.72
2019-04-08 19:00:45 +02:00
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E &quot;08/Apr/2019:(17|18|19)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
5 129.0.79.206
5 41.205.240.21
7 207.46.13.95
7 66.249.79.133
7 66.249.79.135
7 95.108.181.88
8 40.77.167.111
19 157.55.39.164
20 40.77.167.132
370 51.254.16.223
</code></pre></li>
</ul>
2019-04-08 18:55:20 +02:00
2019-04-09 08:33:52 +02:00
<h2 id="2019-04-09">2019-04-09</h2>
<ul>
<li>Linode sent an alert that CGSpace (linode18) was 440% CPU for the last two hours this morning</li>
2019-05-05 15:45:12 +02:00
<li><p>Here are the top IPs in the web server logs around that time:</p>
2019-04-09 08:33:52 +02:00
<pre><code># zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E &quot;09/Apr/2019:(06|07|08)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
18 66.249.79.139
21 157.55.39.160
29 66.249.79.137
38 66.249.79.135
50 34.200.212.137
54 66.249.79.133
100 102.128.190.18
1166 45.5.184.72
4251 45.5.186.2
4895 205.186.128.185
2019-04-09 08:33:52 +02:00
# zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E &quot;09/Apr/2019:(06|07|08)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2019-05-05 15:45:12 +02:00
200 144.48.242.108
202 207.46.13.185
206 18.194.46.84
239 66.249.79.139
246 18.196.196.108
274 31.6.77.23
289 66.249.79.137
312 157.55.39.160
441 66.249.79.135
856 66.249.79.133
</code></pre></li>
<li><p><code>45.5.186.2</code> is at CIAT in Colombia and I see they are mostly making requests to the REST API, but also to XMLUI with the following user agent:</p>
2019-04-09 08:33:52 +02:00
<pre><code>Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/73.0.3683.103 Safari/537.36
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-09 08:33:52 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Database connection usage looks fine:</p>
2019-04-09 08:33:52 +02:00
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
2019-05-05 15:45:12 +02:00
5 dspaceApi
7 dspaceCli
11 dspaceWeb
</code></pre></li>
2019-04-09 08:33:52 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Ironically I do still see some 2 to 10% of CPU steal in <code>iostat 1 10</code></p></li>
<li><p>Leroy from CIAT contacted me to say he knows the team who is making all those requests to CGSpace</p>
2019-04-10 08:48:40 +02:00
<ul>
<li>I told them how to use the REST API to get the CIAT Datasets collection and enumerate its items</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>In other news, Linode staff identified a noisy neighbor sharing our host and migrated it elsewhere last night</p></li>
2019-04-10 08:48:40 +02:00
</ul>
<h2 id="2019-04-10">2019-04-10</h2>
<ul>
<li>Abenet pointed out a possibility of validating funders against the <a href="https://support.crossref.org/hc/en-us/articles/215788143-Funder-data-via-the-API">CrossRef API</a></li>
2019-05-05 15:45:12 +02:00
<li><p>Note that if you use HTTPS and specify a contact address in the API request you have less likelihood of being blocked</p>
2019-04-10 08:48:40 +02:00
<pre><code>$ http 'https://api.crossref.org/funders?query=mercator&amp;mailto=me@cgiar.org'
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-10 08:48:40 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Otherwise, they provide the funder data in <a href="https://www.crossref.org/services/funder-registry/">CSV and RDF format</a></p></li>
<li><p>I did a quick test with the recent IITA records against reconcile-csv in OpenRefine and it matched a few, but the ones that didn&rsquo;t match will need a human to go and do some manual checking and informed decision making&hellip;</p></li>
<li><p>If I want to write a script for this I could use the Python <a href="https://habanero.readthedocs.io/en/latest/modules/crossref.html">habanero library</a>:</p>
2019-04-09 08:33:52 +02:00
2019-04-10 12:44:05 +02:00
<pre><code>from habanero import Crossref
cr = Crossref(mailto=&quot;me@cgiar.org&quot;)
x = cr.funders(query = &quot;mercator&quot;)
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul>
2019-04-10 12:44:05 +02:00
2019-04-11 12:29:52 +02:00
<h2 id="2019-04-11">2019-04-11</h2>
<ul>
2019-04-11 13:23:30 +02:00
<li>Continue proofing IITA&rsquo;s last round of batch uploads from <a href="https://dspacetest.cgiar.org/handle/10568/100333">March on DSpace Test</a> (20193rd.xls)
2019-04-11 12:29:52 +02:00
<ul>
<li>One misspelled country</li>
<li>Three incorrect regions</li>
<li>Potential duplicates (same DOI, similar title, same authors):</li>
<li><a href="https://dspacetest.cgiar.org/handle/10568/100580"><sup>10568</sup>&frasl;<sub>100580</sub></a> and <a href="https://dspacetest.cgiar.org/handle/10568/100579"><sup>10568</sup>&frasl;<sub>100579</sub></a></li>
<li><a href="https://dspacetest.cgiar.org/handle/10568/100444"><sup>10568</sup>&frasl;<sub>100444</sub></a> and <a href="https://dspacetest.cgiar.org/handle/10568/100423"><sup>10568</sup>&frasl;<sub>100423</sub></a></li>
<li>Two DOIs with incorrect URL formatting</li>
<li>Two misspelled IITA subjects</li>
<li>Two authors with smart quotes</li>
<li>Lots of issues with sponsors</li>
<li>One misspelled &ldquo;Peer review&rdquo;</li>
<li>One invalid ISBN that I fixed by Googling the title</li>
<li>Lots of issues with sponsors (German Aid Agency, Swiss Aid Agency, Italian Aid Agency, Dutch Aid Agency, etc)</li>
<li>I validated all the AGROVOC subjects against our latest list with reconcile-csv</li>
<li>About 720 of the 900 terms were matched, then I checked and fixed or deleted the rest manually</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>I captured a few general corrections and deletions for AGROVOC subjects while looking at IITA&rsquo;s records, so I applied them to DSpace Test and CGSpace:</p>
2019-04-11 12:29:52 +02:00
2019-04-11 13:23:30 +02:00
<pre><code>$ ./fix-metadata-values.py -i /tmp/2019-04-11-fix-14-subjects.csv -db dspace -u dspace -p 'fuuu' -f dc.subject -m 57 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-04-11-delete-6-subjects.csv -db dspace -u dspace -p 'fuuu' -m 57 -f dc.subject -d
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-11 12:29:52 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Answer more questions about DOIs and Altmetric scores from WLE</p></li>
<li><p>Answer more questions about DOIs and Altmetric scores from IWMI</p>
2019-04-11 12:29:52 +02:00
<ul>
<li>They can&rsquo;t seem to understand the Altmetric + Twitter flow for associating Handles and DOIs</li>
<li>To make things worse, many of their items DON&rsquo;T have DOIs, so when Altmetric harvests them of course there is no link! - Then, a bunch of their items don&rsquo;t have scores because they never tweeted them!</li>
<li>They added a DOI to this old item <a href="https://cgspace.cgiar.org/handle/10568/97087"><sup>10567</sup>&frasl;<sub>97087</sub></a> this morning and wonder why Altmetric&rsquo;s score hasn&rsquo;t linked with the DOI magically</li>
<li>We should check in a week to see if Altmetric will make the association after one week when they harvest again</li>
</ul></li>
</ul>
2019-04-13 11:15:55 +02:00
<h2 id="2019-04-13">2019-04-13</h2>
<ul>
<li>I copied the <code>statistics</code> and <code>statistics-2018</code> Solr cores from CGSpace to my local machine and watched the Java process in VisualVM while indexing item views and downloads with my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a>:</li>
</ul>
<p><img src="/cgspace-notes/2019/04/visualvm-solr-indexing.png" alt="Java GC during Solr indexing with CMS" /></p>
<ul>
<li>It took about eight minutes to index 784 pages of item views and 268 of downloads, and you can see a clear &ldquo;sawtooth&rdquo; pattern in the garbage collection</li>
<li>I am curious if the GC pattern would be different if I switched from the <code>-XX:+UseConcMarkSweepGC</code> to G1GC</li>
<li>I switched to G1GC and restarted Tomcat but for some reason I couldn&rsquo;t see the Tomcat PID in VisualVM&hellip;
<ul>
<li>Anyways, the indexing process took much longer, perhaps twice as long!</li>
</ul></li>
<li>I tried again with the GC tuning settings from the Solr 4.10.4 release:</li>
</ul>
<p><img src="/cgspace-notes/2019/04/visualvm-solr-indexing-solr-settings.png" alt="Java GC during Solr indexing Solr 4.10.4 settings" /></p>
2019-04-14 15:59:47 +02:00
<h2 id="2019-04-14">2019-04-14</h2>
<ul>
2019-05-05 15:45:12 +02:00
<li><p>Change DSpace Test (linode19) to use the Java GC tuning from the Solr 4.14.4 startup script:</p>
2019-04-14 15:59:47 +02:00
<pre><code>GC_TUNE=&quot;-XX:NewRatio=3 \
2019-05-05 15:45:12 +02:00
-XX:SurvivorRatio=4 \
-XX:TargetSurvivorRatio=90 \
-XX:MaxTenuringThreshold=8 \
-XX:+UseConcMarkSweepGC \
-XX:+UseParNewGC \
-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4 \
-XX:+CMSScavengeBeforeRemark \
-XX:PretenureSizeThreshold=64m \
-XX:+UseCMSInitiatingOccupancyOnly \
-XX:CMSInitiatingOccupancyFraction=50 \
-XX:CMSMaxAbortablePrecleanTime=6000 \
-XX:+CMSParallelRemarkEnabled \
-XX:+ParallelRefProcEnabled&quot;
</code></pre></li>
<li><p>I need to remember to check the Munin JVM graphs in a few days</p></li>
<li><p>It might be placebo, but the site <em>does</em> feel snappier&hellip;</p></li>
2019-04-14 15:59:47 +02:00
</ul>
2019-04-15 11:58:07 +02:00
<h2 id="2019-04-15">2019-04-15</h2>
<ul>
<li>Rework the dspace-statistics-api to use the vanilla Python requests library instead of Solr client
<ul>
<li><a href="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.0.0">Tag version 1.0.0</a> and deploy it on DSpace Test</li>
</ul></li>
2019-04-15 16:42:53 +02:00
<li>Pretty annoying to see CGSpace (linode18) with 2050% CPU steal according to <code>iostat 1 10</code>, though I haven&rsquo;t had any Linode alerts in a few days</li>
2019-05-05 15:45:12 +02:00
<li><p>Abenet sent me a list of ILRI items that don&rsquo;t have CRPs added to them</p>
2019-04-15 16:42:53 +02:00
<ul>
<li>The spreadsheet only had Handles (no IDs), so I&rsquo;m experimenting with using Python in OpenRefine to get the IDs</li>
2019-05-05 15:45:12 +02:00
<li><p>I cloned the handle column and then did a transform to get the IDs from the CGSpace REST API:</p>
2019-04-15 16:42:53 +02:00
<pre><code>import json
import re
import urllib
import urllib2
handle = re.findall('[0-9]+/[0-9]+', value)
url = 'https://cgspace.cgiar.org/rest/handle/' + handle[0]
req = urllib2.Request(url)
req.add_header('User-agent', 'Alan Python bot')
res = urllib2.urlopen(req)
data = json.load(res)
item_id = data['id']
return item_id
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-15 16:42:53 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Luckily none of the items already had CRPs, so I didn&rsquo;t have to worry about them getting removed</p>
2019-04-15 16:42:53 +02:00
<ul>
<li>It would have been much trickier if I had to get the CRPs for the items first, then add the CRPs&hellip;</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>I ran a full Discovery indexing on CGSpace because I didn&rsquo;t do it after all the metadata updates last week:</p>
2019-04-15 11:58:07 +02:00
2019-04-15 22:01:19 +02:00
<pre><code>$ time schedtool -B -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
real 82m45.324s
user 7m33.446s
sys 2m13.463s
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul>
2019-04-15 22:01:19 +02:00
2019-04-16 12:07:33 +02:00
<h2 id="2019-04-16">2019-04-16</h2>
<ul>
<li>Export IITA&rsquo;s community from CGSpace because they want to experiment with importing it into their internal DSpace for some testing or something</li>
</ul>
2019-04-17 12:38:50 +02:00
<h2 id="2019-04-17">2019-04-17</h2>
<ul>
<li>Reading an interesting <a href="https://teaspoon-consulting.com/articles/solr-cache-tuning.html">blog post about Solr caching</a></li>
<li>Did some tests of the dspace-statistics-api on my local DSpace instance with 28 million documents in a sharded statistics core (<code>statistics</code> and <code>statistics-2018</code>) and monitored the memory usage of Tomcat in VisualVM</li>
<li>4GB heap, CMS GC, 512 filter cache, 512 query cache, with 28 million documents in two shards
<ul>
<li>Run 1:</li>
<li>Time: 3.11s user 0.44s system 0% cpu 13:45.07 total</li>
<li>Tomcat (not Solr) max JVM heap usage: 2.04 GiB</li>
<li>Run 2:</li>
<li>Time: 3.23s user 0.43s system 0% cpu 13:46.10 total</li>
<li>Tomcat (not Solr) max JVM heap usage: 2.06 GiB</li>
<li>Run 3:</li>
<li>Time: 3.23s user 0.42s system 0% cpu 13:14.70 total</li>
<li>Tomcat (not Solr) max JVM heap usage: 2.13 GiB</li>
<li><code>filterCache</code> size: 482, <code>cumulative_lookups</code>: 7062712, <code>cumulative_hits</code>: 167903, <code>cumulative_hitratio</code>: 0.02</li>
<li>queryResultCache size: 2</li>
</ul></li>
<li>4GB heap, CMS GC, 1024 filter cache, 512 query cache, with 28 million documents in two shards
<ul>
<li>Run 1:</li>
<li>Time: 2.92s user 0.39s system 0% cpu 12:33.08 total</li>
<li>Tomcat (not Solr) max JVM heap usage: 2.16 GiB</li>
<li>Run 2:</li>
<li>Time: 3.10s user 0.39s system 0% cpu 12:25.32 total</li>
<li>Tomcat (not Solr) max JVM heap usage: 2.07 GiB</li>
<li>Run 3:</li>
<li>Time: 3.29s user 0.36s system 0% cpu 11:53.47 total</li>
<li>Tomcat (not Solr) max JVM heap usage: 2.08 GiB</li>
<li><code>filterCache</code> size: 951, <code>cumulative_lookups</code>: 7062712, <code>cumulative_hits</code>: 254379, <code>cumulative_hitratio</code>: 0.04</li>
</ul></li>
<li>4GB heap, CMS GC, 2048 filter cache, 512 query cache, with 28 million documents in two shards
<ul>
<li>Run 1:</li>
<li>Time: 2.90s user 0.48s system 0% cpu 10:37.31 total</li>
<li>Tomcat max JVM heap usage: 1.96 GiB</li>
<li><code>filterCache</code> size: 1901, <code>cumulative_lookups</code>: 2354237, <code>cumulative_hits</code>: 180111, <code>cumulative_hitratio</code>: 0.08</li>
<li>Run 2:</li>
<li>Time: 2.97s user 0.39s system 0% cpu 10:40.06 total</li>
<li>Tomcat max JVM heap usage: 2.09 GiB</li>
<li><code>filterCache</code> size: 1901, <code>cumulative_lookups</code>: 4708473, <code>cumulative_hits</code>: 360068, <code>cumulative_hitratio</code>: 0.08</li>
<li>Run 3:</li>
<li>Time: 3.28s user 0.37s system 0% cpu 10:49.56 total</li>
<li>Tomcat max JVM heap usage: 2.05 GiB</li>
<li><code>filterCache</code> size: 1901, <code>cumulative_lookups</code>: 7062712, <code>cumulative_hits</code>: 540020, <code>cumulative_hitratio</code>: 0.08</li>
</ul></li>
<li>4GB heap, CMS GC, 4096 filter cache, 512 query cache, with 28 million documents in two shards
<ul>
<li>Run 1:</li>
<li>Time: 2.88s user 0.35s system 0% cpu 8:29.55 total</li>
<li>Tomcat max JVM heap usage: 2.15 GiB</li>
<li><code>filterCache</code> size: 3770, <code>cumulative_lookups</code>: 2354237, <code>cumulative_hits</code>: 414512, <code>cumulative_hitratio</code>: 0.18</li>
<li>Run 2:</li>
<li>Time: 3.01s user 0.38s system 0% cpu 9:15.65 total</li>
<li>Tomcat max JVM heap usage: 2.17 GiB</li>
<li><code>filterCache</code> size: 3945, <code>cumulative_lookups</code>: 4708473, <code>cumulative_hits</code>: 829093, <code>cumulative_hitratio</code>: 0.18</li>
<li>Run 3:</li>
<li>Time: 3.01s user 0.40s system 0% cpu 9:01.31 total</li>
<li>Tomcat max JVM heap usage: 2.07 GiB</li>
<li><code>filterCache</code> size: 3770, <code>cumulative_lookups</code>: 7062712, <code>cumulative_hits</code>: 1243632, <code>cumulative_hitratio</code>: 0.18</li>
</ul></li>
<li>The biggest takeaway I have is that this workload benefits from a larger <code>filterCache</code> (for Solr fq parameter), but barely uses the <code>queryResultCache</code> (for Solr q parameter) at all
<ul>
<li>The number of hits goes up and the time taken decreases when we increase the <code>filterCache</code>, and total JVM heap memory doesn&rsquo;t seem to increase much at all</li>
<li>I guess the <code>queryResultCache</code> size is always 2 because I&rsquo;m only doing two queries: <code>type:0</code> and <code>type:2</code> (downloads and views, respectively)</li>
</ul></li>
<li>Here is the general pattern of running three sequential indexing runs as seen in VisualVM while monitoring the Tomcat process:</li>
</ul>
<p><img src="/cgspace-notes/2019/04/visualvm-solr-indexing-4096-filterCache.png" alt="VisualVM Tomcat 4096 filterCache" /></p>
<ul>
<li>I ran one test with a <code>filterCache</code> of 16384 to try to see if I could make the Tomcat JVM memory balloon, but actually it <em>drastically</em> increased the performance and memory usage of the dspace-statistics-api indexer</li>
<li>4GB heap, CMS GC, 16384 filter cache, 512 query cache, with 28 million documents in two shards
<ul>
<li>Run 1:</li>
<li>Time: 2.85s user 0.42s system 2% cpu 2:28.92 total</li>
<li>Tomcat max JVM heap usage: 1.90 GiB</li>
<li><code>filterCache</code> size: 14851, <code>cumulative_lookups</code>: 2354237, <code>cumulative_hits</code>: 2331186, <code>cumulative_hitratio</code>: 0.99</li>
<li>Run 2:</li>
<li>Time: 2.90s user 0.37s system 2% cpu 2:23.50 total</li>
<li>Tomcat max JVM heap usage: 1.27 GiB</li>
<li><code>filterCache</code> size: 15834, <code>cumulative_lookups</code>: 4708476, <code>cumulative_hits</code>: 4664762, <code>cumulative_hitratio</code>: 0.99</li>
<li>Run 3:</li>
<li>Time: 2.93s user 0.39s system 2% cpu 2:26.17 total</li>
<li>Tomcat max JVM heap usage: 1.05 GiB</li>
<li><code>filterCache</code> size: 15248, <code>cumulative_lookups</code>: 7062715, <code>cumulative_hits</code>: 6998267, <code>cumulative_hitratio</code>: 0.99</li>
</ul></li>
<li>The JVM garbage collection graph is MUCH flatter, and memory usage is much lower (not to mention a drop in GC-related CPU usage)!</li>
</ul>
<p><img src="/cgspace-notes/2019/04/visualvm-solr-indexing-16384-filterCache.png" alt="VisualVM Tomcat 16384 filterCache" /></p>
2019-04-17 14:16:27 +02:00
<ul>
<li>I will deploy this <code>filterCache</code> setting on DSpace Test (linode19)</li>
<li>Run all system updates on DSpace Test (linode19) and reboot it</li>
2019-04-18 11:31:49 +02:00
<li>Lots of CPU steal going on still on CGSpace (linode18):</li>
</ul>
<p><img src="/cgspace-notes/2019/04/cpu-week3.png" alt="CPU usage week" /></p>
<h2 id="2019-04-18">2019-04-18</h2>
<ul>
2019-04-18 18:00:15 +02:00
<li>I&rsquo;ve been trying to copy the <code>statistics-2018</code> Solr core from CGSpace to DSpace Test since yesterday, but the network speed is like 20KiB/sec
<ul>
<li>I opened a support ticket to ask Linode to investigate</li>
<li>They asked me to send an <code>mtr</code> report from Fremont to Frankfurt and vice versa</li>
</ul></li>
2019-04-18 11:40:54 +02:00
<li>Deploy Tomcat 7.0.94 on DSpace Test (linode19)
<ul>
<li>Also, I realized that the CMS GC changes I deployed a few days ago were ignored by Tomcat because of something with how Ansible formatted the options string</li>
<li>I needed to use the &ldquo;folded&rdquo; YAML variable format <code>&gt;-</code> (with the dash so it doesn&rsquo;t add a return at the end)</li>
</ul></li>
2019-04-18 18:00:15 +02:00
<li>UptimeRobot says that CGSpace went &ldquo;down&rdquo; this afternoon, but I looked at the CPU steal with <code>iostat 1 10</code> and it&rsquo;s in the 50s and 60s
<ul>
<li>The munin graph shows a lot of CPU steal (red) currently (and over all during the week):</li>
</ul></li>
</ul>
<p><img src="/cgspace-notes/2019/04/cpu-week4.png" alt="CPU usage week" /></p>
<ul>
<li>I opened a ticket with Linode to migrate us somewhere
<ul>
<li>They agreed to migrate us to a quieter host</li>
</ul></li>
2019-04-17 14:16:27 +02:00
</ul>
2019-04-20 10:48:26 +02:00
<h2 id="2019-04-20">2019-04-20</h2>
<ul>
<li>Linode agreed to move CGSpace (linode18) to a new machine shortly after I filed my ticket about CPU steal two days ago and now the load is much more sane:</li>
</ul>
<p><img src="/cgspace-notes/2019/04/cpu-week5.png" alt="CPU usage week" /></p>
<ul>
<li>For future reference, Linode mentioned that they consider CPU steal above 8% to be significant</li>
2019-05-05 15:45:12 +02:00
<li><p>Regarding the other Linode issue about speed, I did a test with <code>iperf</code> between linode18 and linode19:</p>
2019-04-20 11:20:12 +02:00
<pre><code># iperf -s
------------------------------------------------------------
Server listening on TCP port 5001
TCP window size: 85.3 KByte (default)
------------------------------------------------------------
[ 4] local 45.79.x.x port 5001 connected with 139.162.x.x port 51378
------------------------------------------------------------
Client connecting to 139.162.x.x, TCP port 5001
TCP window size: 85.0 KByte (default)
------------------------------------------------------------
[ 5] local 45.79.x.x port 36440 connected with 139.162.x.x port 5001
[ ID] Interval Transfer Bandwidth
[ 5] 0.0-10.2 sec 172 MBytes 142 Mbits/sec
[ 4] 0.0-10.5 sec 202 MBytes 162 Mbits/sec
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-20 11:20:12 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Even with the software firewalls disabled the rsync speed was low, so it&rsquo;s not a rate limiting issue</p></li>
<li><p>I also tried to download a file over HTTPS from CGSpace to DSpace Test, but it was capped at 20KiB/sec</p>
2019-04-20 11:20:12 +02:00
<ul>
<li>I updated the Linode issue with this information</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>I&rsquo;m going to try to switch the kernel to the latest upstream (5.0.8) instead of Linode&rsquo;s latest x86_64</p>
2019-04-20 11:24:02 +02:00
<ul>
<li>Nope, still 20KiB/sec</li>
</ul></li>
2019-04-20 10:48:26 +02:00
</ul>
2019-04-21 14:31:15 +02:00
<h2 id="2019-04-21">2019-04-21</h2>
<ul>
<li>Deploy Solr 4.10.4 on CGSpace (linode18)</li>
<li>Deploy Tomcat 7.0.94 on CGSpace</li>
<li>Deploy dspace-statistics-api v1.0.0 on CGSpace</li>
2019-04-21 17:52:00 +02:00
<li>Linode support replicated the results I had from the network speed testing and said they don&rsquo;t know why it&rsquo;s so slow
<ul>
<li>They offered to live migrate the instance to another host to see if that helps</li>
</ul></li>
2019-04-21 14:31:15 +02:00
</ul>
2019-04-22 15:09:58 +02:00
<h2 id="2019-04-22">2019-04-22</h2>
<ul>
<li>Abenet pointed out <a href="https://hdl.handle.net/10568/97912">an item</a> that doesn&rsquo;t have an Altmetric score on CGSpace, but has a score of 343 in the CGSpace Altmetric dashboard
<ul>
<li>I tweeted the Handle to see if it will pick it up&hellip;</li>
<li>Like clockwork, after fifteen minutes there was a donut showing on CGSpace</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>I want to get rid of this annoying warning that is constantly in our DSpace logs:</p>
2019-04-22 15:09:58 +02:00
<pre><code>2019-04-08 19:02:31,770 WARN org.dspace.xoai.services.impl.xoai.DSpaceRepositoryConfiguration @ { OAI 2.0 :: DSpace } Not able to retrieve the dspace.oai.url property from oai.cfg. Falling back to request address
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-22 15:09:58 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Apparently it happens once per request, which can be at least 1,500 times per day according to the DSpace logs on CGSpace (linode18):</p>
2019-04-22 15:09:58 +02:00
<pre><code>$ grep -c 'Falling back to request address' dspace.log.2019-04-20
dspace.log.2019-04-20:1515
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-22 15:09:58 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I will fix it in <code>dspace/config/modules/oai.cfg</code></p></li>
<li><p>Linode says that it is likely that the host CGSpace (linode18) is on is showing signs of hardware failure and they recommended that I migrate the VM to a new host</p>
2019-04-22 15:09:58 +02:00
<ul>
<li>I told them to migrate it at 04:00:00AM Frankfurt time, when nobody in East Africa, Europe, or South America should be using the server</li>
</ul></li>
</ul>
2019-04-23 12:04:37 +02:00
<h2 id="2019-04-23">2019-04-23</h2>
<ul>
<li>One blog post says that there is <a href="https://kvaes.wordpress.com/2017/07/01/what-azure-virtual-machine-size-should-i-pick/">no overprovisioning in Azure</a>:</li>
</ul>
<blockquote cite="https://kvaes.wordpress.com/2017/07/01/what-azure-virtual-machine-size-should-i-pick/">In Azure, with one exception being the A0, there is no overprovisioning… Each physical cores is only supporting one virtual core.</blockquote>
<ul>
<li>Perhaps that&rsquo;s why the <a href="https://azure.microsoft.com/en-us/pricing/details/virtual-machines/linux/">Azure pricing</a> is so expensive!</li>
<li>Add a privacy page to CGSpace
<ul>
<li>The work was mostly similar to the About page at <code>/page/about</code>, but in addition to adding i18n strings etc, I had to add the logic for the trail to <code>dspace-xmlui-mirage2/src/main/webapp/xsl/preprocess/general.xsl</code></li>
</ul></li>
</ul>
2019-04-24 15:50:24 +02:00
<h2 id="2019-04-24">2019-04-24</h2>
<ul>
<li>Linode migrated CGSpace (linode18) to a new host, but I am still getting poor performance when copying data to DSpace Test (linode19)
<ul>
<li>I asked them if we can migrate DSpace Test to a new host</li>
<li>They migrated DSpace Test to a new host and the rsync speed from Frankfurt was still capped at 20KiB/sec&hellip;</li>
<li>I booted DSpace Test to a rescue CD and tried the rsync from CGSpace there too, but it was still capped at 20KiB/sec&hellip;</li>
2019-04-24 16:15:13 +02:00
<li>I copied the 18GB <code>statistics-2018</code> Solr core from Frankfurt to a Linode in London at 15MiB/sec, then from the London one to DSpace Test in Fremont at 15MiB/sec&hellip; so WTF us up with Frankfurt→Fremont?!</li>
2019-04-24 15:50:24 +02:00
</ul></li>
<li>Finally upload the 218 IITA items from March to CGSpace
<ul>
<li>Abenet and I had to do a little bit more work to correct the metadata of one item that appeared to be a duplicate, but really just had the wrong DOI</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>While I was uploading the IITA records I noticed that twenty of the records Sisay uploaded in 2018-09 had double Handles (<code>dc.identifier.uri</code>)</p>
2019-04-24 15:50:24 +02:00
<ul>
<li>According to my notes in 2018-09 I had noticed this when he uploaded the records and told him to remove them, but he didn&rsquo;t&hellip;</li>
2019-05-05 15:45:12 +02:00
<li><p>I exported the IITA community as a CSV then used <code>csvcut</code> to extract the two URI columns and identify and fix the records:</p>
2019-04-24 15:50:24 +02:00
<pre><code>$ csvcut -c id,dc.identifier.uri,'dc.identifier.uri[]' ~/Downloads/2019-04-24-IITA.csv &gt; /tmp/iita.csv
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-24 15:50:24 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Carlos Tejo from the Land Portal had been emailing me this week to ask about the old REST API that Tsega was building in 2017</p>
2019-04-24 15:50:24 +02:00
<ul>
<li>I told him we never finished it, and that he should try to use the <code>/items/find-by-metadata-field</code> endpoint, with the caveat that you need to match the language attribute exactly (ie &ldquo;en&rdquo;, &ldquo;en_US&rdquo;, null, etc)</li>
<li>I asked him how many terms they are interested in, as we could probably make it easier by normalizing the language attributes of these fields (it would help us anyways)</li>
2019-05-05 15:45:12 +02:00
<li><p>He says he&rsquo;s getting HTTP 401 errors when trying to search for CPWF subject terms, which I can reproduce:</p>
2019-04-24 15:50:24 +02:00
2019-04-24 17:49:55 +02:00
<pre><code>$ curl -f -H &quot;accept: application/json&quot; -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/items/find-by-metadata-field&quot; -d '{&quot;key&quot;:&quot;cg.subject.cpwf&quot;, &quot;value&quot;:&quot;WATER MANAGEMENT&quot;,&quot;language&quot;: &quot;en_US&quot;}'
curl: (22) The requested URL returned error: 401
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-24 17:49:55 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Note that curl only shows the HTTP 401 error if you use <code>-f</code> (fail), and only then if you <em>don&rsquo;t</em> include <code>-s</code></p>
2019-04-24 17:49:55 +02:00
<ul>
<li>I see there are about 1,000 items using CPWF subject &ldquo;WATER MANAGEMENT&rdquo; in the database, so there should definitely be results</li>
2019-05-05 15:45:12 +02:00
<li><p>The breakdown of <code>text_lang</code> fields used in those items is 942:</p>
2019-04-24 17:49:55 +02:00
<pre><code>dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT' AND text_lang='en_US';
2019-05-05 15:45:12 +02:00
count
2019-04-24 17:49:55 +02:00
-------
2019-05-05 15:45:12 +02:00
376
2019-04-24 17:49:55 +02:00
(1 row)
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT' AND text_lang='';
2019-05-05 15:45:12 +02:00
count
2019-04-24 17:49:55 +02:00
-------
2019-05-05 15:45:12 +02:00
149
2019-04-24 17:49:55 +02:00
(1 row)
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT' AND text_lang IS NULL;
2019-05-05 15:45:12 +02:00
count
2019-04-24 17:49:55 +02:00
-------
2019-05-05 15:45:12 +02:00
417
2019-04-24 17:49:55 +02:00
(1 row)
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-24 17:49:55 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I see that the HTTP 401 issue seems to be a bug due to an item that the user doesn&rsquo;t have permission to access&hellip; from the DSpace log:</p>
2019-04-24 17:49:55 +02:00
<pre><code>2019-04-24 08:11:51,129 INFO org.dspace.rest.ItemsResource @ Looking for item with metadata(key=cg.subject.cpwf,value=WATER MANAGEMENT, language=en_US).
2019-04-24 08:11:51,231 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous::view_item:handle=10568/72448
2019-04-24 08:11:51,238 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous::view_item:handle=10568/72491
2019-04-24 08:11:51,243 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous::view_item:handle=10568/75703
2019-04-24 08:11:51,252 ERROR org.dspace.rest.ItemsResource @ User(anonymous) has not permission to read item!
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-24 17:49:55 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Nevertheless, if I request using the <code>null</code> language I get 1020 results, plus 179 for a blank language attribute:</p>
2019-04-24 17:49:55 +02:00
<pre><code>$ curl -s -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/items/find-by-metadata-field&quot; -d '{&quot;key&quot;:&quot;cg.subject.cpwf&quot;, &quot;value&quot;:&quot;WATER MANAGEMENT&quot;,&quot;language&quot;: null}' | jq length
1020
$ curl -s -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/items/find-by-metadata-field&quot; -d '{&quot;key&quot;:&quot;cg.subject.cpwf&quot;, &quot;value&quot;:&quot;WATER MANAGEMENT&quot;,&quot;language&quot;: &quot;&quot;}' | jq length
179
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-24 17:49:55 +02:00
2019-05-05 15:45:12 +02:00
<li><p>This is weird because I see 9421156 items with &ldquo;WATER MANAGEMENT&rdquo; (depending on wildcard matching for errors in subject spelling):</p>
2019-04-24 17:49:55 +02:00
<pre><code>dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT';
2019-05-05 15:45:12 +02:00
count
2019-04-24 17:49:55 +02:00
-------
2019-05-05 15:45:12 +02:00
942
2019-04-24 17:49:55 +02:00
(1 row)
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value LIKE '%WATER MANAGEMENT%';
2019-05-05 15:45:12 +02:00
count
2019-04-24 17:49:55 +02:00
-------
2019-05-05 15:45:12 +02:00
1156
2019-04-24 17:49:55 +02:00
(1 row)
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-24 17:49:55 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I sent a message to the dspace-tech mailing list to ask for help</p></li>
2019-04-24 17:49:55 +02:00
</ul>
2019-04-25 22:06:39 +02:00
<h2 id="2019-04-25">2019-04-25</h2>
<ul>
<li>Peter pointed out that we need to remove Delicious and Google+ from our social sharing links
<ul>
<li>Also, it would be nice if we could include the item title in the shared link</li>
<li>I created an issue on GitHub to track this (<a href="https://github.com/ilri/DSpace/issues/419">#419</a>)</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>I tested the REST API after logging in with my super admin account and I was able to get results for the problematic query:</p>
2019-04-25 22:06:39 +02:00
<pre><code>$ curl -f -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/login&quot; -d '{&quot;email&quot;:&quot;example@me.com&quot;,&quot;password&quot;:&quot;fuuuuu&quot;}'
$ curl -f -H &quot;Content-Type: application/json&quot; -H &quot;rest-dspace-token: b43d41a6-5ac1-455d-b49a-616b8debc25b&quot; -X GET &quot;https://dspacetest.cgiar.org/rest/status&quot;
$ curl -f -H &quot;rest-dspace-token: b43d41a6-5ac1-455d-b49a-616b8debc25b&quot; -H &quot;Content-Type: application/json&quot; -X POST &quot;https://dspacetest.cgiar.org/rest/items/find-by-metadata-field&quot; -d '{&quot;key&quot;:&quot;cg.subject.cpwf&quot;, &quot;value&quot;:&quot;WATER MANAGEMENT&quot;,&quot;language&quot;: &quot;en_US&quot;}'
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-25 22:06:39 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I created a normal user for Carlos to try as an unprivileged user:</p>
2019-04-25 22:06:39 +02:00
<pre><code>$ dspace user --add --givenname Carlos --surname Tejo --email blah@blah.com --password 'ddmmdd'
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-25 22:06:39 +02:00
2019-05-05 15:45:12 +02:00
<li><p>But still I get the HTTP 401 and I have no idea which item is causing it</p></li>
<li><p>I enabled more verbose logging in <code>ItemsResource.java</code> and now I can at least see the item ID that causes the failure&hellip;</p>
2019-04-25 22:06:39 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>The item is not even in the archive, but somehow it is discoverable</p>
2019-04-25 22:06:39 +02:00
<pre><code>dspace=# SELECT * FROM item WHERE item_id=74648;
2019-05-05 15:45:12 +02:00
item_id | submitter_id | in_archive | withdrawn | last_modified | owning_collection | discoverable
2019-04-25 22:06:39 +02:00
---------+--------------+------------+-----------+----------------------------+-------------------+--------------
2019-05-05 15:45:12 +02:00
74648 | 113 | f | f | 2016-03-30 09:00:52.131+00 | | t
2019-04-25 22:06:39 +02:00
(1 row)
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-25 22:06:39 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I tried to delete the item in the web interface, and it seems successful, but I can still access the item in the admin interface, and nothing changes in PostgreSQL</p></li>
<li><p>Meet with CodeObia to see progress on AReS version 2</p></li>
<li><p>Marissa Van Epp asked me to add a few new metadata values to their Phase II Project Tags field (cg.identifier.ccafsprojectpii)</p>
2019-04-25 22:06:39 +02:00
<ul>
<li>I created a <a href="https://github.com/ilri/DSpace/pull/420">pull request</a> for it and will do it the next time I run updates on CGSpace</li>
</ul></li>
2019-05-05 15:45:12 +02:00
<li><p>Communicate with Carlos Tejo from the Land Portal about the <code>/items/find-by-metadata-value</code> endpoint</p></li>
<li><p>Run all system updates on DSpace Test (linode19) and reboot it</p></li>
2019-04-25 22:06:39 +02:00
</ul>
2019-04-26 11:16:02 +02:00
<h2 id="2019-04-26">2019-04-26</h2>
<ul>
2019-05-05 15:45:12 +02:00
<li><p>Export a list of authors for Peter to look through:</p>
2019-04-26 11:16:02 +02:00
2019-05-27 11:06:48 +02:00
<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/2019-04-26-all-authors.csv with csv header;
2019-04-26 11:16:02 +02:00
COPY 65752
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul>
2019-04-26 11:16:02 +02:00
2019-04-28 18:07:51 +02:00
<h2 id="2019-04-28">2019-04-28</h2>
<ul>
2019-05-05 15:45:12 +02:00
<li><p>Still trying to figure out the issue with the items that cause the REST API&rsquo;s <code>/items/find-by-metadata-value</code> endpoint to throw an exception</p>
2019-04-28 18:07:51 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>I made the item private in the UI and then I see in the UI and PostgreSQL that it is no longer discoverable:</p>
2019-04-28 18:07:51 +02:00
<pre><code>dspace=# SELECT * FROM item WHERE item_id=74648;
2019-05-05 15:45:12 +02:00
item_id | submitter_id | in_archive | withdrawn | last_modified | owning_collection | discoverable
2019-04-28 18:07:51 +02:00
---------+--------------+------------+-----------+----------------------------+-------------------+--------------
2019-05-05 15:45:12 +02:00
74648 | 113 | f | f | 2019-04-28 08:48:52.114-07 | | f
2019-04-28 18:07:51 +02:00
(1 row)
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-28 18:07:51 +02:00
2019-05-05 15:45:12 +02:00
<li><p>And I tried the <code>curl</code> command from above again, but I still get the HTTP 401 and and the same error in the DSpace log:</p>
2019-04-28 18:07:51 +02:00
<pre><code>2019-04-28 08:53:07,170 ERROR org.dspace.rest.ItemsResource @ User(anonymous) has not permission to read item(id=74648)!
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-28 18:07:51 +02:00
2019-05-05 15:45:12 +02:00
<li><p>I even tried to &ldquo;expunge&rdquo; the item using an <a href="https://wiki.duraspace.org/display/DSDOC5x/Batch+Metadata+Editing#BatchMetadataEditing-Performing'actions'onitems">action in CSV</a>, and it said &ldquo;EXPUNGED!&rdquo; but the item is still there&hellip;</p></li>
2019-04-28 18:07:51 +02:00
</ul>
2019-04-30 10:39:09 +02:00
<h2 id="2019-04-30">2019-04-30</h2>
<ul>
<li>Send mail to the dspace-tech mailing list to ask about the item expunge issue</li>
2019-05-05 15:45:12 +02:00
<li><p>Delete and re-create Podman container for dspacedb after pulling a new PostgreSQL container:</p>
2019-04-30 10:39:09 +02:00
<pre><code>$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
2019-05-05 15:45:12 +02:00
</code></pre></li>
2019-04-30 10:39:09 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Carlos from LandPortal asked if I could export CGSpace in a machine-readable format so I think I&rsquo;ll try to do a CSV</p>
2019-04-30 10:39:09 +02:00
<ul>
2019-05-05 15:45:12 +02:00
<li><p>In order to make it easier for him to understand the CSV I will normalize the text languages (minus the provenance field) on my local development instance before exporting:</p>
2019-04-30 10:39:09 +02:00
<pre><code>dspace=# SELECT DISTINCT text_lang, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id != 28 GROUP BY text_lang;
2019-05-05 15:45:12 +02:00
text_lang | count
2019-04-30 10:39:09 +02:00
-----------+---------
2019-05-05 15:45:12 +02:00
| 358647
* | 11
E. | 1
en | 1635
en_US | 602312
es | 12
es_ES | 2
ethnob | 1
fr | 2
spa | 2
| 1074345
2019-04-30 10:39:09 +02:00
(11 rows)
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('ethnob', 'en', '*', 'E.', '');
UPDATE 360295
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IS NULL;
UPDATE 1074345
dspace=# UPDATE metadatavalue SET text_lang='es_ES' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('es', 'spa');
UPDATE 14
2019-05-05 15:45:12 +02:00
</code></pre></li>
</ul></li>
2019-04-30 10:39:09 +02:00
2019-05-05 15:45:12 +02:00
<li><p>Then I exported the whole repository as CSV, imported it into OpenRefine, removed a few unneeded columns, exported it, zipped it down to 36MB, and emailed a link to Carlos</p></li>
<li><p>In other news, while I was looking through the CSV in OpenRefine I saw lots of weird values in some fields&hellip; we should check, for example:</p>
2019-04-30 10:39:09 +02:00
<ul>
<li>issue dates</li>
<li>items missing handles</li>
<li>authorship types</li>
</ul></li>
</ul>
2019-04-01 08:02:18 +02:00
<!-- vim: set sw=2 ts=2: -->
</article>
</div> <!-- /.blog-main -->
<aside class="col-sm-3 ml-auto blog-sidebar">
<section class="sidebar-module">
<h4>Recent Posts</h4>
<ol class="list-unstyled">
2019-10-01 16:31:40 +02:00
<li><a href="/cgspace-notes/2019-10/">October, 2019</a></li>
2019-09-01 09:41:30 +02:00
<li><a href="/cgspace-notes/2019-09/">September, 2019</a></li>
<li><a href="/cgspace-notes/2019-08/">August, 2019</a></li>
2019-08-04 21:49:04 +02:00
<li><a href="/cgspace-notes/2019-07/">July, 2019</a></li>
<li><a href="/cgspace-notes/2019-06/">June, 2019</a></li>
2019-04-01 08:02:18 +02:00
</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">
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2019-04-01 08:02:18 +02:00
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