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362 lines
12 KiB
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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="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-04/" />
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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="2019-04-05T22:22:41+03:00"/>
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<meta name="twitter:card" content="summary"/>
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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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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 name="generator" content="Hugo 0.54.0" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"datePublished": "2019-04-01T09:00:43+03:00",
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"dateModified": "2019-04-05T22:22:41+03:00",
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"author": {
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2019-04/">
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<title>April, 2019 | CGSpace Notes</title>
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<header class="blog-header">
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<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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</div>
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<article class="blog-post">
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-04/">April, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-04-01T09:00:43+03:00">Mon Apr 01, 2019</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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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
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<ul>
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<li>They asked if we had plans to enable RDF support in CGSpace</li>
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</ul></li>
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<li>There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
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<ul>
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<li>I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!</li>
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</ul></li>
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</ul>
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<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 $9}' | sort | uniq -c | sort -n | tail -n 5
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4432 200
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</code></pre>
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<ul>
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<li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li>
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<li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li>
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</ul>
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<pre><code>$ ./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
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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>
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<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></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></li>
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</ul>
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<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 > /tmp/2019-04-03-orcid-ids.txt
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</code></pre>
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<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><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>
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<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><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>
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<ul>
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<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>
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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><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>
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<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><code>$ grep 'org.dspace.statistics.SolrLogger @ Updating' /home/cgspace.cgiar.org/log/dspace.log.2019-04-03 | awk '{print $11}' | sort | uniq -c
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1
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3 http://localhost:8081/solr//statistics-2017
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5662 http://localhost:8081/solr//statistics-2018
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</code></pre>
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<ul>
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<li>I will have to keep an eye on it because nothing should be updating 2018 stats in 2019…</li>
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</ul>
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<h2 id="2019-04-05">2019-04-05</h2>
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<ul>
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<li>Uptime Robot reported that CGSpace (linode18) went down tonight</li>
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<li>I see there are lots of PostgreSQL connections:</li>
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</ul>
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<pre><code>$ 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>
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<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><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>
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<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></li>
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</ul>
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<pre><code>statistics-2017: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
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</code></pre>
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<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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<!-- vim: set sw=2 ts=2: -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
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<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
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<li><a href="/cgspace-notes/2019-02/">February, 2019</a></li>
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<li><a href="/cgspace-notes/2019-01/">January, 2019</a></li>
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<li><a href="/cgspace-notes/2018-12/">December, 2018</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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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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