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<meta property="og:title" content="April, 2019" />
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<meta property="og:description" content="2019-04-01
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Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
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They asked if we had plans to enable RDF support in CGSpace
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There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
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I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!
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# 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 $9}' | sort | uniq -c | sort -n | tail -n 5
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4432 200
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In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
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Apply country and region corrections and deletions on DSpace Test and CGSpace:
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$ ./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
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$ ./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
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$ ./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
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$ ./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
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" />
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<meta property="article:published_time" content="2019-04-01T09:00:43+03:00" />
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<meta property="article:modified_time" content="2021-08-18T15:29:31+03:00" />
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<meta name="twitter:title" content="April, 2019"/>
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<meta name="twitter:description" content="2019-04-01
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||
|
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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!
|
||
|
||
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||
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# 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 $9}' | sort | uniq -c | sort -n | tail -n 5
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4432 200
|
||
|
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In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
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Apply country and region corrections and deletions on DSpace Test and CGSpace:
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||
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$ ./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
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$ ./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
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$ ./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
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$ ./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
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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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>
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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>
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<time datetime="2019-04-01T09:00:43+03:00">Mon Apr 01, 2019</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</header>
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<h2 id="2019-04-01">2019-04-01</h2>
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<ul>
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<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 tabindex="0"><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 $9}' | sort | uniq -c | sort -n | tail -n 5
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4432 200
|
||
</code></pre><ul>
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||
<li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li>
|
||
<li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ ./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
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$ ./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
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$ ./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
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$ ./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
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</code></pre><h2 id="2019-04-02">2019-04-02</h2>
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<ul>
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<li>CTA says the Amazon IPs are AWS gateways for real user traffic</li>
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<li>I was trying to add Felix Shaw’s account back to the Administrators group on DSpace Test, but I couldn’t find his name in the user search of the groups page
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<ul>
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<li>If I searched for “Felix” or “Shaw” I saw other matches, included one for his personal email address!</li>
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<li>I ended up finding him via searching for his email address</li>
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</ul>
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</li>
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</ul>
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<h2 id="2019-04-03">2019-04-03</h2>
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<ul>
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<li>Maria from Bioversity emailed me a list of new ORCID identifiers for their researchers so I will add them to our controlled vocabulary
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<ul>
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<li>First I need to extract the ones that are unique from their list compared to our existing one:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><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 > /tmp/2019-04-03-orcid-ids.txt
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</code></pre><ul>
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<li>We currently have 1177 unique ORCID identifiers, and this brings our total to 1237!</li>
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<li>Next I will resolve all their names using my <code>resolve-orcids.py</code> script:</li>
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</ul>
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<pre tabindex="0"><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><ul>
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<li>After that I added the XML formatting, formatted the file with tidy, and sorted the names in vim</li>
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<li>One user’s name has changed so I will update those using my <code>fix-metadata-values.py</code> script:</li>
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</ul>
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<pre tabindex="0"><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
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</code></pre><ul>
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<li>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>)</li>
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<li>A few days ago I noticed some weird update process for the statistics-2018 Solr core and I see it’s still going:</li>
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</ul>
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<pre tabindex="0"><code>2019-04-03 16:34:02,262 INFO org.dspace.statistics.SolrLogger @ Updating : 1754500/21701 docs in http://localhost:8081/solr//statistics-2018
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</code></pre><ul>
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<li>Interestingly, there are 5666 occurences, and they are mostly for the 2018 core:</li>
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</ul>
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<pre tabindex="0"><code>$ grep 'org.dspace.statistics.SolrLogger @ Updating' /home/cgspace.cgiar.org/log/dspace.log.2019-04-03 | awk '{print $11}' | sort | uniq -c
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1
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3 http://localhost:8081/solr//statistics-2017
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5662 http://localhost:8081/solr//statistics-2018
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</code></pre><ul>
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<li>I will have to keep an eye on it because nothing should be updating 2018 stats in 2019…</li>
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</ul>
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<h2 id="2019-04-05">2019-04-05</h2>
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<ul>
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<li>Uptime Robot reported that CGSpace (linode18) went down tonight</li>
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<li>I see there are lots of PostgreSQL connections:</li>
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</ul>
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<pre tabindex="0"><code>$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
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5 dspaceApi
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10 dspaceCli
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250 dspaceWeb
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</code></pre><ul>
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<li>I still see those weird messages about updating the statistics-2018 Solr core:</li>
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</ul>
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<pre tabindex="0"><code>2019-04-05 21:06:53,770 INFO org.dspace.statistics.SolrLogger @ Updating : 2444600/21697 docs in http://localhost:8081/solr//statistics-2018
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</code></pre><ul>
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<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>
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</ul>
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<p><img src="/cgspace-notes/2019/04/cpu-week.png" alt="CPU usage week"></p>
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<ul>
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<li>The other thing visible there is that the past few days the load has spiked to 500% and I don’t think it’s a coincidence that the Solr updating thing is happening…</li>
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<li>I ran all system updates and rebooted the server
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<ul>
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<li>The load was lower on the server after reboot, but Solr didn’t come back up properly according to the Solr Admin UI:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>statistics-2017: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
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</code></pre><ul>
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<li>I restarted it again and all the Solr cores came up properly…</li>
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</ul>
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<h2 id="2019-04-06">2019-04-06</h2>
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<ul>
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<li>Udana asked why item <a href="https://cgspace.cgiar.org/handle/10568/91278">10568/91278</a> didn’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
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<ul>
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<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>
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<li>I tweeted the item and I assume this will link the Handle with the DOI in the system</li>
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<li>Twenty minutes later I see the same Altmetric score (9) on CGSpace</li>
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</ul>
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</li>
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<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>
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</ul>
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<pre tabindex="0"><code># zcat --force /var/log/nginx/{access,error,library-access}.log /var/log/nginx/{access,error,library-access}.log.1 | grep -E "06/Apr/2019:(06|07|08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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222 18.195.78.144
|
||
245 207.46.13.58
|
||
303 207.46.13.194
|
||
328 66.249.79.33
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||
564 207.46.13.210
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566 66.249.79.62
|
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575 40.77.167.66
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1803 66.249.79.59
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2834 2a01:4f8:140:3192::2
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9623 45.5.184.72
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# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "06/Apr/2019:(06|07|08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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31 66.249.79.62
|
||
41 207.46.13.210
|
||
42 40.77.167.66
|
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54 42.113.50.219
|
||
132 66.249.79.59
|
||
785 2001:41d0:d:1990::
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||
1164 45.5.184.72
|
||
2014 50.116.102.77
|
||
4267 45.5.186.2
|
||
4893 205.186.128.185
|
||
</code></pre><ul>
|
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<li><code>45.5.184.72</code> is in Colombia so it’s probably CIAT, and I see they are indeed trying to get crawl the Discover pages on CIAT’s datasets collection:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>GET /handle/10568/72970/discover?filtertype_0=type&filtertype_1=author&filter_relational_operator_1=contains&filter_relational_operator_0=equals&filter_1=&filter_0=Dataset&filtertype=dateIssued&filter_relational_operator=equals&filter=2014
|
||
</code></pre><ul>
|
||
<li>Their user agent is the one I added to the badbots list in nginx last week: “GuzzleHttp/6.3.3 curl/7.47.0 PHP/7.0.30-0ubuntu0.16.04.1”</li>
|
||
<li>They made 22,000 requests to Discover on this collection today alone (and it’s only 11AM):</li>
|
||
</ul>
|
||
<pre tabindex="0"><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep "06/Apr/2019" | 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 tabindex="0"><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep "05/Apr/2019" | 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 "05/Apr/2019" | grep 45.5.184.72 | grep -E '/handle/[0-9]+/[0-9]+/discover' | awk '{print $9}' | sort | uniq -c
|
||
142 200
|
||
43489 503
|
||
</code></pre><ul>
|
||
<li>I need to find a contact at CIAT to tell them to use the REST API rather than crawling Discover</li>
|
||
<li>Maria from Bioversity recommended that we use the phrase “AGROVOC subject” instead of “Subject” in Listings and Reports
|
||
<ul>
|
||
<li>I made a pull request to update this and merged it to the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/418">#418</a>)</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
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<h2 id="2019-04-07">2019-04-07</h2>
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<ul>
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<li>Looking into the impact of harvesters like <code>45.5.184.72</code>, I see in Solr that this user is not categorized as a bot so it definitely impacts the usage stats by some tens of thousands <em>per day</em></li>
|
||
<li>Last week CTA switched their frontend code to use HEAD requests instead of GET requests for bitstreams
|
||
<ul>
|
||
<li>I am trying to see if these are registered as downloads in Solr or not</li>
|
||
<li>I see 96,925 downloads from their AWS gateway IPs in 2019-03:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ 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)&fq=statistics_type%3Aview&fq=bundleName%3AORIGINAL&fq=dateYearMonth%3A2019-03&rows=0&wt=json&indent=true'
|
||
{
|
||
"response": {
|
||
"docs": [],
|
||
"numFound": 96925,
|
||
"start": 0
|
||
},
|
||
"responseHeader": {
|
||
"QTime": 1,
|
||
"params": {
|
||
"fq": [
|
||
"statistics_type:view",
|
||
"bundleName:ORIGINAL",
|
||
"dateYearMonth:2019-03"
|
||
],
|
||
"indent": "true",
|
||
"q": "type:0 AND (ip:18.196.196.108 OR ip:18.195.78.144 OR ip:18.195.218.6)",
|
||
"rows": "0",
|
||
"wt": "json"
|
||
},
|
||
"status": 0
|
||
}
|
||
}
|
||
</code></pre><ul>
|
||
<li>Strangely I don’t see many hits in 2019-04:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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)&fq=statistics_type%3Aview&fq=bundleName%3AORIGINAL&fq=dateYearMonth%3A2019-04&rows=0&wt=json&indent=true'
|
||
{
|
||
"response": {
|
||
"docs": [],
|
||
"numFound": 38,
|
||
"start": 0
|
||
},
|
||
"responseHeader": {
|
||
"QTime": 1,
|
||
"params": {
|
||
"fq": [
|
||
"statistics_type:view",
|
||
"bundleName:ORIGINAL",
|
||
"dateYearMonth:2019-04"
|
||
],
|
||
"indent": "true",
|
||
"q": "type:0 AND (ip:18.196.196.108 OR ip:18.195.78.144 OR ip:18.195.218.6)",
|
||
"rows": "0",
|
||
"wt": "json"
|
||
},
|
||
"status": 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 tabindex="0"><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 tabindex="0"><code>78.x.x.x - - [07/Apr/2019:01:38:35 -0700] "GET /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1" 200 68078 "-" "HTTPie/1.0.2"
|
||
78.x.x.x - - [07/Apr/2019:01:39:01 -0700] "HEAD /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1" 200 0 "-" "HTTPie/1.0.2"
|
||
</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’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 tabindex="0"><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’t been modified in 24 hours, so I tried to start the “optimize” process from the Admin UI and I see this in the Solr log:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><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>… very weird
|
||
<ul>
|
||
<li>I don’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.lyrasis.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 tabindex="0"><code>$ http --print b 'http://localhost:8080/solr/statistics/select?q=type%3A0+AND+time%3A2019-04-07*&fq=statistics_type%3Aview&fq=isInternal%3Atrue&rows=0&wt=json&indent=true'
|
||
{
|
||
"response": {
|
||
"docs": [],
|
||
"numFound": 909,
|
||
"start": 0
|
||
},
|
||
"responseHeader": {
|
||
"QTime": 0,
|
||
"params": {
|
||
"fq": [
|
||
"statistics_type:view",
|
||
"isInternal:true"
|
||
],
|
||
"indent": "true",
|
||
"q": "type:0 AND time:2019-04-07*",
|
||
"rows": "0",
|
||
"wt": "json"
|
||
},
|
||
"status": 0
|
||
}
|
||
}
|
||
</code></pre><ul>
|
||
<li>I confirmed the same on CGSpace itself after making one HEAD request</li>
|
||
<li>So I’m pretty sure it’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’s server as of 2018-04-01</li>
|
||
<li>Now I made 100 requests and I see them in the Solr statistics… 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 10–30 percent right now…</li>
|
||
<li>The load average is super high right now, as I’ve noticed the last few times UptimeRobot said that CGSpace went down:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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 tabindex="0"><code># zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E "07/Apr/2019:(18|19|20)" | 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 "07/Apr/2019:(18|19|20)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
||
3 66.249.79.62
|
||
3 66.249.83.196
|
||
4 207.46.13.86
|
||
5 82.145.222.150
|
||
6 2a01:4f9:2b:1263::2
|
||
6 41.204.190.40
|
||
7 35.174.176.49
|
||
10 40.77.167.21
|
||
11 194.246.119.6
|
||
11 66.249.79.59
|
||
</code></pre><ul>
|
||
<li><code>45.5.184.72</code> is CIAT, who I already blocked and am waiting to hear from</li>
|
||
<li><code>2a01:4f8:140:3192::2</code> is BLEXbot, which should be handled by the Tomcat Crawler Session Manager Valve</li>
|
||
<li><code>2408:8214:7a00:868f:7c1e:e0f3:20c6:c142</code> is some stupid Chinese bot making malicious POST requests</li>
|
||
<li>There are free database connections in the pool:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ 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 “down” 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’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 tabindex="0"><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’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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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’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 tabindex="0"><code># zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E "08/Apr/2019:(17|18|19)" | 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 "08/Apr/2019:(17|18|19)" | 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 tabindex="0"><code># zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "09/Apr/2019:(06|07|08)" | 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 "09/Apr/2019:(06|07|08)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
||
200 144.48.242.108
|
||
202 207.46.13.185
|
||
206 18.194.46.84
|
||
239 66.249.79.139
|
||
246 18.196.196.108
|
||
274 31.6.77.23
|
||
289 66.249.79.137
|
||
312 157.55.39.160
|
||
441 66.249.79.135
|
||
856 66.249.79.133
|
||
</code></pre><ul>
|
||
<li><code>45.5.186.2</code> is at CIAT in Colombia and I see they are mostly making requests to the REST API, but also to XMLUI with the following user agent:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/73.0.3683.103 Safari/537.36
|
||
</code></pre><ul>
|
||
<li>Database connection usage looks fine:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ 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 tabindex="0"><code>$ http 'https://api.crossref.org/funders?query=mercator&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’t match will need a human to go and do some manual checking and informed decision making…</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 tabindex="0"><code>from habanero import Crossref
|
||
cr = Crossref(mailto="me@cgiar.org")
|
||
x = cr.funders(query = "mercator")
|
||
</code></pre><h2 id="2019-04-11">2019-04-11</h2>
|
||
<ul>
|
||
<li>Continue proofing IITA’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):
|
||
<ul>
|
||
<li><a href="https://dspacetest.cgiar.org/handle/10568/100580">10568/100580</a> and <a href="https://dspacetest.cgiar.org/handle/10568/100579">10568/100579</a></li>
|
||
<li><a href="https://dspacetest.cgiar.org/handle/10568/100444">10568/100444</a> and <a href="https://dspacetest.cgiar.org/handle/10568/100423">10568/100423</a></li>
|
||
</ul>
|
||
</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 “Peer review”</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
|
||
<ul>
|
||
<li>About 720 of the 900 terms were matched, then I checked and fixed or deleted the rest manually</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>I captured a few general corrections and deletions for AGROVOC subjects while looking at IITA’s records, so I applied them to DSpace Test and CGSpace:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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’t seem to understand the Altmetric + Twitter flow for associating Handles and DOIs</li>
|
||
<li>To make things worse, many of their items DON’T have DOIs, so when Altmetric harvests them of course there is no link! - Then, a bunch of their items don’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">10567/97087</a> this morning and wonder why Altmetric’s score hasn’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 “sawtooth” 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’t see the Tomcat PID in VisualVM…
|
||
<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 4.10.4 startup script:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>GC_TUNE="-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"
|
||
</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…</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>
|
||
<li>Pretty annoying to see CGSpace (linode18) with 20–50% CPU steal according to <code>iostat 1 10</code>, though I haven’t had any Linode alerts in a few days</li>
|
||
<li>Abenet sent me a list of ILRI items that don’t have CRPs added to them
|
||
<ul>
|
||
<li>The spreadsheet only had Handles (no IDs), so I’m experimenting with using Python in OpenRefine to get the IDs</li>
|
||
<li>I cloned the handle column and then did a transform to get the IDs from the CGSpace REST API:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><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
|
||
</code></pre><ul>
|
||
<li>Luckily none of the items already had CRPs, so I didn’t have to worry about them getting removed
|
||
<ul>
|
||
<li>It would have been much trickier if I had to get the CRPs for the items first, then add the CRPs…</li>
|
||
</ul>
|
||
</li>
|
||
<li>I ran a full Discovery indexing on CGSpace because I didn’t do it after all the metadata updates last week:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ time schedtool -B -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
||
|
||
real 82m45.324s
|
||
user 7m33.446s
|
||
sys 2m13.463s
|
||
</code></pre><h2 id="2019-04-16">2019-04-16</h2>
|
||
<ul>
|
||
<li>Export IITA’s community from CGSpace because they want to experiment with importing it into their internal DSpace for some testing or something</li>
|
||
</ul>
|
||
<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:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 2:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 3:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>4GB heap, CMS GC, 1024 filter cache, 512 query cache, with 28 million documents in two shards
|
||
<ul>
|
||
<li>Run 1:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 2:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 3:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>4GB heap, CMS GC, 2048 filter cache, 512 query cache, with 28 million documents in two shards
|
||
<ul>
|
||
<li>Run 1:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 2:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 3:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>4GB heap, CMS GC, 4096 filter cache, 512 query cache, with 28 million documents in two shards
|
||
<ul>
|
||
<li>Run 1:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 2:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 3:
|
||
<ul>
|
||
<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>
|
||
</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’t seem to increase much at all</li>
|
||
<li>I guess the <code>queryResultCache</code> size is always 2 because I’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:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 2:
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
<li>Run 3:
|
||
<ul>
|
||
<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>
|
||
</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>
|
||
<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>
|
||
<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>
|
||
<li>I’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>
|
||
<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 “folded” YAML variable format <code>>-</code> (with the dash so it doesn’t add a return at the end)</li>
|
||
</ul>
|
||
</li>
|
||
<li>UptimeRobot says that CGSpace went “down” this afternoon, but I looked at the CPU steal with <code>iostat 1 10</code> and it’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>
|
||
</ul>
|
||
<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>
|
||
<li>Regarding the other Linode issue about speed, I did a test with <code>iperf</code> between linode18 and linode19:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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
|
||
</code></pre><ul>
|
||
<li>Even with the software firewalls disabled the rsync speed was low, so it’s not a rate limiting issue</li>
|
||
<li>I also tried to download a file over HTTPS from CGSpace to DSpace Test, but it was capped at 20KiB/sec
|
||
<ul>
|
||
<li>I updated the Linode issue with this information</li>
|
||
</ul>
|
||
</li>
|
||
<li>I’m going to try to switch the kernel to the latest upstream (5.0.8) instead of Linode’s latest x86_64
|
||
<ul>
|
||
<li>Nope, still 20KiB/sec</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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>
|
||
<li>Linode support replicated the results I had from the network speed testing and said they don’t know why it’s so slow
|
||
<ul>
|
||
<li>They offered to live migrate the instance to another host to see if that helps</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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’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…</li>
|
||
<li>Like clockwork, after fifteen minutes there was a donut showing on CGSpace</li>
|
||
</ul>
|
||
</li>
|
||
<li>I want to get rid of this annoying warning that is constantly in our DSpace logs:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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
|
||
</code></pre><ul>
|
||
<li>Apparently it happens once per request, which can be at least 1,500 times per day according to the DSpace logs on CGSpace (linode18):</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ grep -c 'Falling back to request address' dspace.log.2019-04-20
|
||
dspace.log.2019-04-20:1515
|
||
</code></pre><ul>
|
||
<li>I will fix it in <code>dspace/config/modules/oai.cfg</code></li>
|
||
<li>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
|
||
<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>
|
||
<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>
|
||
<!-- raw HTML omitted -->
|
||
<ul>
|
||
<li>Perhaps that’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>
|
||
<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…</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…</li>
|
||
<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… so WTF us up with Frankfurt→Fremont?!</li>
|
||
</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>
|
||
<li>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>)
|
||
<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’t…</li>
|
||
<li>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:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ csvcut -c id,dc.identifier.uri,'dc.identifier.uri[]' ~/Downloads/2019-04-24-IITA.csv > /tmp/iita.csv
|
||
</code></pre><ul>
|
||
<li>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
|
||
<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 “en”, “en_US”, 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>
|
||
<li>He says he’s getting HTTP 401 errors when trying to search for CPWF subject terms, which I can reproduce:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ curl -f -H "accept: application/json" -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": "en_US"}'
|
||
curl: (22) The requested URL returned error: 401
|
||
</code></pre><ul>
|
||
<li>Note that curl only shows the HTTP 401 error if you use <code>-f</code> (fail), and only then if you <em>don’t</em> include <code>-s</code>
|
||
<ul>
|
||
<li>I see there are about 1,000 items using CPWF subject “WATER MANAGEMENT” in the database, so there should definitely be results</li>
|
||
<li>The breakdown of <code>text_lang</code> fields used in those items is 942:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><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';
|
||
count
|
||
-------
|
||
376
|
||
(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='';
|
||
count
|
||
-------
|
||
149
|
||
(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;
|
||
count
|
||
-------
|
||
417
|
||
(1 row)
|
||
</code></pre><ul>
|
||
<li>I see that the HTTP 401 issue seems to be a bug due to an item that the user doesn’t have permission to access… from the DSpace log:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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!
|
||
</code></pre><ul>
|
||
<li>Nevertheless, if I request using the <code>null</code> language I get 1020 results, plus 179 for a blank language attribute:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ curl -s -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": null}' | jq length
|
||
1020
|
||
$ curl -s -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": ""}' | jq length
|
||
179
|
||
</code></pre><ul>
|
||
<li>This is weird because I see 942–1156 items with “WATER MANAGEMENT” (depending on wildcard matching for errors in subject spelling):</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT';
|
||
count
|
||
-------
|
||
942
|
||
(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%';
|
||
count
|
||
-------
|
||
1156
|
||
(1 row)
|
||
</code></pre><ul>
|
||
<li>I sent a message to the dspace-tech mailing list to ask for help</li>
|
||
</ul>
|
||
<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>
|
||
<li>I tested the REST API after logging in with my super admin account and I was able to get results for the problematic query:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ curl -f -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/login" -d '{"email":"example@me.com","password":"fuuuuu"}'
|
||
$ curl -f -H "Content-Type: application/json" -H "rest-dspace-token: b43d41a6-5ac1-455d-b49a-616b8debc25b" -X GET "https://dspacetest.cgiar.org/rest/status"
|
||
$ curl -f -H "rest-dspace-token: b43d41a6-5ac1-455d-b49a-616b8debc25b" -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": "en_US"}'
|
||
</code></pre><ul>
|
||
<li>I created a normal user for Carlos to try as an unprivileged user:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ dspace user --add --givenname Carlos --surname Tejo --email blah@blah.com --password 'ddmmdd'
|
||
</code></pre><ul>
|
||
<li>But still I get the HTTP 401 and I have no idea which item is causing it</li>
|
||
<li>I enabled more verbose logging in <code>ItemsResource.java</code> and now I can at least see the item ID that causes the failure…
|
||
<ul>
|
||
<li>The item is not even in the archive, but somehow it is discoverable</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# SELECT * FROM item WHERE item_id=74648;
|
||
item_id | submitter_id | in_archive | withdrawn | last_modified | owning_collection | discoverable
|
||
---------+--------------+------------+-----------+----------------------------+-------------------+--------------
|
||
74648 | 113 | f | f | 2016-03-30 09:00:52.131+00 | | t
|
||
(1 row)
|
||
</code></pre><ul>
|
||
<li>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</li>
|
||
<li>Meet with CodeObia to see progress on AReS version 2</li>
|
||
<li>Marissa Van Epp asked me to add a few new metadata values to their Phase II Project Tags field (cg.identifier.ccafsprojectpii)
|
||
<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>
|
||
<li>Communicate with Carlos Tejo from the Land Portal about the <code>/items/find-by-metadata-value</code> endpoint</li>
|
||
<li>Run all system updates on DSpace Test (linode19) and reboot it</li>
|
||
</ul>
|
||
<h2 id="2019-04-26">2019-04-26</h2>
|
||
<ul>
|
||
<li>Export a list of authors for Peter to look through:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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;
|
||
COPY 65752
|
||
</code></pre><h2 id="2019-04-28">2019-04-28</h2>
|
||
<ul>
|
||
<li>Still trying to figure out the issue with the items that cause the REST API’s <code>/items/find-by-metadata-value</code> endpoint to throw an exception
|
||
<ul>
|
||
<li>I made the item private in the UI and then I see in the UI and PostgreSQL that it is no longer discoverable:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# SELECT * FROM item WHERE item_id=74648;
|
||
item_id | submitter_id | in_archive | withdrawn | last_modified | owning_collection | discoverable
|
||
---------+--------------+------------+-----------+----------------------------+-------------------+--------------
|
||
74648 | 113 | f | f | 2019-04-28 08:48:52.114-07 | | f
|
||
(1 row)
|
||
</code></pre><ul>
|
||
<li>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:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>2019-04-28 08:53:07,170 ERROR org.dspace.rest.ItemsResource @ User(anonymous) has not permission to read item(id=74648)!
|
||
</code></pre><ul>
|
||
<li>I even tried to “expunge” the item using an <a href="https://wiki.lyrasis.org/display/DSDOC5x/Batch+Metadata+Editing#BatchMetadataEditing-Performing'actions'onitems">action in CSV</a>, and it said “EXPUNGED!” but the item is still there…</li>
|
||
</ul>
|
||
<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>
|
||
<li>Delete and re-create Podman container for dspacedb after pulling a new PostgreSQL container:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
|
||
</code></pre><ul>
|
||
<li>Carlos from LandPortal asked if I could export CGSpace in a machine-readable format so I think I’ll try to do a CSV
|
||
<ul>
|
||
<li>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:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# SELECT DISTINCT text_lang, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id != 28 GROUP BY text_lang;
|
||
text_lang | count
|
||
-----------+---------
|
||
| 358647
|
||
* | 11
|
||
E. | 1
|
||
en | 1635
|
||
en_US | 602312
|
||
es | 12
|
||
es_ES | 2
|
||
ethnob | 1
|
||
fr | 2
|
||
spa | 2
|
||
| 1074345
|
||
(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
|
||
</code></pre><ul>
|
||
<li>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</li>
|
||
<li>In other news, while I was looking through the CSV in OpenRefine I saw lots of weird values in some fields… we should check, for example:
|
||
<ul>
|
||
<li>issue dates</li>
|
||
<li>items missing handles</li>
|
||
<li>authorship types</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<!-- raw HTML omitted -->
|
||
|
||
|
||
|
||
|
||
|
||
</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">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2022-01/">January, 2022</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-12/">December, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-11/">November, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-10/">October, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-09/">September, 2021</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
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|
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</aside>
|
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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||
<p>
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<a href="#">Back to top</a>
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</body>
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