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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
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
4432 200
In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
Apply country and region corrections and deletions on DSpace Test and CGSpace:
$ ./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
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<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
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
4432 200
In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
Apply country and region corrections and deletions on DSpace Test and CGSpace:
$ ./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
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-04/">April, 2019</a></h2>
<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>
<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>
<li>There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
<ul>
<li>I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!</li>
</ul></li>
</ul>
<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 $9}' | sort | uniq -c | sort -n | tail -n 5
4432 200
</code></pre>
<ul>
<li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li>
<li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li>
</ul>
<pre><code>$ ./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
</code></pre>
<h2 id="2019-04-02">2019-04-02</h2>
<ul>
<li>CTA says the Amazon IPs are AWS gateways for real user traffic</li>
<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>
</ul>
<h2 id="2019-04-03">2019-04-03</h2>
<ul>
<li>Maria from Bioversity emailed me a list of new ORCID identifiers for their researchers so I will add them to our controlled vocabulary
<ul>
<li>First I need to extract the ones that are unique from their list compared to our existing one:</li>
</ul></li>
</ul>
<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
</code></pre>
<ul>
<li>We currently have 1177 unique ORCID identifiers, and this brings our total to 1237!</li>
<li>Next I will resolve all their names using my <code>resolve-orcids.py</code> script:</li>
</ul>
<pre><code>$ ./resolve-orcids.py -i /tmp/2019-04-03-orcid-ids.txt -o 2019-04-03-orcid-ids.txt -d
</code></pre>
<ul>
<li>After that I added the XML formatting, formatted the file with tidy, and sorted the names in vim</li>
<li>One user&rsquo;s name has changed so I will update those using my <code>fix-metadata-values.py</code> script:</li>
</ul>
<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
</code></pre>
<ul>
<li>I created a pull request and merged the changes to the 5_x-prod branch (<a href="https://github.com/ilri/DSpace/pull/417">#417</a>)</li>
<li>A few days ago I noticed some weird update process for the statistics-2018 Solr core and I see it&rsquo;s still going:</li>
</ul>
<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
</code></pre>
<ul>
<li>Interestingly, there are 5666 occurences, and they are mostly for the 2018 core:</li>
</ul>
<pre><code>$ grep 'org.dspace.statistics.SolrLogger @ Updating' /home/cgspace.cgiar.org/log/dspace.log.2019-04-03 | awk '{print $11}' | sort | uniq -c
1
3 http://localhost:8081/solr//statistics-2017
5662 http://localhost:8081/solr//statistics-2018
</code></pre>
<ul>
<li>I will have to keep an eye on it because nothing should be updating 2018 stats in 2019&hellip;</li>
</ul>
<h2 id="2019-04-05">2019-04-05</h2>
<ul>
<li>Uptime Robot reported that CGSpace (linode18) went down tonight</li>
<li>I see there are lots of PostgreSQL connections:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
10 dspaceCli
250 dspaceWeb
</code></pre>
<ul>
<li>I still see those weird messages about updating the statistics-2018 Solr core:</li>
</ul>
<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
</code></pre>
<ul>
<li>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:</li>
</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>
<li>I ran all system updates and rebooted the server
<ul>
<li>The load was lower on the server after reboot, but Solr didn&rsquo;t come back up properly according to the Solr Admin UI:</li>
</ul></li>
</ul>
<pre><code>statistics-2017: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
</code></pre>
<ul>
<li>I restarted it again and all the Solr cores came up properly&hellip;</li>
</ul>
<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>
<li>Twenty minutes later I see the same Altmetric score (9) on CGSpace</li>
</ul></li>
<li>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:</li>
</ul>
<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
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
# 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
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>
<ul>
<li><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:</li>
</ul>
<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
</code></pre>
<ul>
<li>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;</li>
<li>They made 22,000 requests to Discover on this collection today alone (and it&rsquo;s only 11AM):</li>
</ul>
<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
22077 /handle/10568/72970/discover
</code></pre>
<ul>
<li>Yesterday they made 43,000 requests and we actually blocked most of them:</li>
</ul>
<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
43631 /handle/10568/72970/discover
# 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 $9}' | sort | uniq -c
142 200
43489 503
</code></pre>
<ul>
<li>I need to find a contact at CIAT to tell them to use the REST API rather than crawling Discover</li>
<li>Maria from Bioversity recommended that we use the phrase &ldquo;AGROVOC subject&rdquo; instead of &ldquo;Subject&rdquo; in Listings and Reports
<ul>
<li>I made a pull request to update this and merged it to the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/418">#418</a>)</li>
</ul></li>
</ul>
<h2 id="2019-04-07">2019-04-07</h2>
<ul>
<li>Looking into the impact of harvesters like <code>45.5.184.72</code>, I see in Solr that this user is not categorized as a bot so it definitely impacts the usage stats by some tens of thousands <em>per day</em></li>
<li>Last week CTA switched their frontend code to use HEAD requests instead of GET requests for bitstreams
<ul>
<li>I am trying to see if these are registered as downloads in Solr or not</li>
<li>I see 96,925 downloads from their AWS gateway IPs in 2019-03:</li>
</ul></li>
</ul>
<pre><code>$ 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'
{
&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
}
}
</code></pre>
<ul>
<li>Strangely I don&rsquo;t see many hits in 2019-04:</li>
</ul>
<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'
{
&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;
},
&quot;status&quot;: 0
}
}
</code></pre>
<ul>
<li>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:</li>
</ul>
<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
</code></pre>
<ul>
<li>And from the server side, the nginx logs show:</li>
</ul>
<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;
</code></pre>
<ul>
<li>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
<ul>
<li>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:</li>
</ul></li>
</ul>
<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
</code></pre>
<ul>
<li>So my inclination is that both HEAD and GET requests are registered as views as far as Solr and DSpace are concerned
<ul>
<li>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:</li>
</ul></li>
</ul>
<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}
</code></pre>
<ul>
<li>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
<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>
<li>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>)</li>
<li>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):</li>
</ul>
<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'
{
&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;
},
&quot;status&quot;: 0
}
}
</code></pre>
<ul>
<li>I confirmed the same on CGSpace itself after making one HEAD request</li>
<li>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
<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>
<li>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
<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>
<li>Holy shit, all this is actually because of the GeoIP1 deprecation and a missing <code>GeoLiteCity.dat</code>
<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>
<li>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;</li>
<li>The load average is super high right now, as I&rsquo;ve noticed the last few times UptimeRobot said that CGSpace went down:</li>
</ul>
<pre><code>$ cat /proc/loadavg
10.70 9.17 8.85 18/633 4198
</code></pre>
<ul>
<li>According to the server logs there is actually not much going on right now:</li>
</ul>
<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
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
# 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 $1}' | sort | uniq -c | sort -n | tail -n 10
3 66.249.79.62
3 66.249.83.196
4 207.46.13.86
5 82.145.222.150
6 2a01:4f9:2b:1263::2
6 41.204.190.40
7 35.174.176.49
10 40.77.167.21
11 194.246.119.6
11 66.249.79.59
</code></pre>
<ul>
<li><code>45.5.184.72</code> is CIAT, who I already blocked and am waiting to hear from</li>
<li><code>2a01:4f8:140:3192::2</code> is BLEXbot, which should be handled by the Tomcat Crawler Session Manager Valve</li>
<li><code>2408:8214:7a00:868f:7c1e:e0f3:20c6:c142</code> is some stupid Chinese bot making malicious POST requests</li>
<li>There are free database connections in the pool:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
7 dspaceCli
23 dspaceWeb
</code></pre>
<ul>
<li>It seems that the issue with CGSpace being &ldquo;down&rdquo; is actually because of CPU steal again!!!</li>
<li>I opened a ticket with support and asked them to migrate the VM to a less busy host</li>
</ul>
<h2 id="2019-04-08">2019-04-08</h2>
<ul>
<li>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)
<ul>
<li>Lots of problems with affiliations, I had to correct about sixty of them</li>
<li>I used lein to host the latest CSV of our affiliations for OpenRefine to reconcile against:</li>
</ul></li>
</ul>
<pre><code>$ lein run ~/src/git/DSpace/2019-02-22-affiliations.csv name id
</code></pre>
<ul>
<li>After matching the values and creating some new matches I had trouble remembering how to copy the reconciled values to a new column
<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>
<li>I ended up using this GREL expression to copy all values to a new column:</li>
</ul></li>
</ul>
<pre><code>if(cell.recon.matched, cell.recon.match.name, value)
</code></pre>
<ul>
<li>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</li>
<li>I also noticed a handful of errors in our current list of affiliations so I corrected them:</li>
</ul>
<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
</code></pre>
<ul>
<li>We should create a new list of affiliations to update our controlled vocabulary again</li>
<li>I dumped a list of the top 1500 affiliations:</li>
</ul>
<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
</code></pre>
<ul>
<li>Fix a few more messed up affiliations that have return characters in them (use Ctrl-V Ctrl-M to re-create control character):</li>
</ul>
<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%';
</code></pre>
<ul>
<li>I noticed a bunch of subjects and affiliations that use stylized apostrophes so I will export those and then batch update them:</li>
</ul>
<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
</code></pre>
<ul>
<li>I cleaned them up in OpenRefine and then applied the fixes on CGSpace and DSpace Test:</li>
</ul>
<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
</code></pre>
<ul>
<li>UptimeRobot said that CGSpace (linode18) went down tonight
<ul>
<li>The load average is at <code>9.42, 8.87, 7.87</code></li>
<li>I looked at PostgreSQL and see shitloads of connections there:</li>
</ul></li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
7 dspaceCli
250 dspaceWeb
</code></pre>
<ul>
<li>On a related note I see connection pool errors in the DSpace log:</li>
</ul>
<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].
</code></pre>
<ul>
<li>But still I see 10 to 30% CPU steal in <code>iostat</code> that is also reflected in the Munin graphs:</li>
</ul>
<p><img src="/cgspace-notes/2019/04/cpu-week2.png" alt="CPU usage week" /></p>
<ul>
<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>
<li>The web server logs are not very busy:</li>
</ul>
<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
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
# 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
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>
<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>
<li>Here are the top IPs in the web server logs around that time:</li>
</ul>
<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
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
# 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 $1}' | sort | uniq -c | sort -n | tail -n 10
200 144.48.242.108
202 207.46.13.185
206 18.194.46.84
239 66.249.79.139
246 18.196.196.108
274 31.6.77.23
289 66.249.79.137
312 157.55.39.160
441 66.249.79.135
856 66.249.79.133
</code></pre>
<ul>
<li><code>45.5.186.2</code> is at CIAT in Colombia and I see they are mostly making requests to the REST API, but also to XMLUI with the following user agent:</li>
</ul>
<pre><code>Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/73.0.3683.103 Safari/537.36
</code></pre>
<ul>
<li>Database connection usage looks fine:</li>
</ul>
<pre><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
7 dspaceCli
11 dspaceWeb
</code></pre>
<ul>
<li>Ironically I do still see some 2 to 10% of CPU steal in <code>iostat 1 10</code></li>
<li>Leroy from CIAT contacted me to say he knows the team who is making all those requests to CGSpace
<ul>
<li>I told them how to use the REST API to get the CIAT Datasets collection and enumerate its items</li>
</ul></li>
<li>In other news, Linode staff identified a noisy neighbor sharing our host and migrated it elsewhere last night</li>
</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>
<li>Note that if you use HTTPS and specify a contact address in the API request you have less likelihood of being blocked</li>
</ul>
<pre><code>$ http 'https://api.crossref.org/funders?query=mercator&amp;mailto=me@cgiar.org'
</code></pre>
<ul>
<li>Otherwise, they provide the funder data in <a href="https://www.crossref.org/services/funder-registry/">CSV and RDF format</a></li>
<li>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;</li>
<li>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>:</li>
</ul>
<pre><code>from habanero import Crossref
cr = Crossref(mailto=&quot;me@cgiar.org&quot;)
x = cr.funders(query = &quot;mercator&quot;)
</code></pre>
<h2 id="2019-04-11">2019-04-11</h2>
<ul>
<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)
<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>
<li>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:</li>
</ul>
<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
</code></pre>
<ul>
<li>Answer more questions about DOIs and Altmetric scores from WLE</li>
<li>Answer more questions about DOIs and Altmetric scores from IWMI
<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>
<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>
<h2 id="2019-04-14">2019-04-14</h2>
<ul>
<li>Change DSpace Test (linode19) to use the Java GC tuning from the Solr 4.14.4 startup script:</li>
</ul>
<pre><code>GC_TUNE=&quot;-XX:NewRatio=3 \
-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>
<ul>
<li>I need to remember to check the Munin JVM graphs in a few days</li>
<li>It might be placebo, but the site <em>does</em> feel snappier&hellip;</li>
</ul>
<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>
</ul>
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