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<meta property="og:title" content="July, 2019" />
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<meta property="og:description" content="2019-07-01
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Create an “AfricaRice books and book chapters” collection on CGSpace for AfricaRice
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Last month Sisay asked why the following “most popular” statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
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DSpace Test
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CGSpace
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Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
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<meta name="twitter:title" content="July, 2019"/>
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<meta name="twitter:description" content="2019-07-01
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Create an “AfricaRice books and book chapters” collection on CGSpace for AfricaRice
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Last month Sisay asked why the following “most popular” statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
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DSpace Test
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CGSpace
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Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
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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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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-07/">July, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-07-01T12:13:51+03:00">Mon Jul 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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<h2 id="2019-07-01">2019-07-01</h2>
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<ul>
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<li>Create an “AfricaRice books and book chapters” collection on CGSpace for AfricaRice</li>
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<li>Last month Sisay asked why the following “most popular” statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
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<ul>
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<li><a href="https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&time_filter_end_date=01%2F12%2F2018">DSpace Test</a></li>
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<li><a href="https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&time_filter_end_date=01%2F12%2F2018">CGSpace</a></li>
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</ul></li>
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<li>Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community</li>
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</ul>
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<ul>
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<li>If I change the parameters to 2019 I see stats, so I’m really thinking it has something to do with the sharded yearly Solr statistics cores
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<ul>
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<li>I checked the Solr admin UI and I see all Solr cores loaded, so I don’t know what it could be</li>
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<li>When I check the Atmire content and usage module it seems obvious that there is a problem with the old cores because I dont have anything before 2019-01</li>
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</ul></li>
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</ul>
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<p><img src="/cgspace-notes/2019/07/atmire-cua-2018-missing.png" alt="Atmire CUA 2018 stats missing" /></p>
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<ul>
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<li>I don’t see anyone logged in right now so I’m going to try to restart Tomcat and see if the stats are accessible after Solr comes back up</li>
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<li><p>I decided to run all system updates on the server (linode18) and reboot it</p>
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<ul>
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<li>After rebooting Tomcat came back up, but the the Solr statistics cores were not all loaded</li>
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<li><p>The error is always (with a different core):</p>
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<pre><code>org.apache.solr.common.SolrException: Error CREATEing SolrCore 'statistics-2010': Unable to create core [statistics-2010] Caused by: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2010/data/index/write.lock
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</code></pre></li>
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</ul></li>
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<li><p>I restarted Tomcat <em>ten times</em> and it never worked…</p></li>
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<li><p>I tried to stop Tomcat and delete the write locks:</p>
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<pre><code># systemctl stop tomcat7
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# find /dspace/solr/statistics* -iname "*.lock" -print -delete
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/dspace/solr/statistics/data/index/write.lock
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/dspace/solr/statistics-2010/data/index/write.lock
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/dspace/solr/statistics-2011/data/index/write.lock
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/dspace/solr/statistics-2012/data/index/write.lock
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/dspace/solr/statistics-2013/data/index/write.lock
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/dspace/solr/statistics-2014/data/index/write.lock
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/dspace/solr/statistics-2015/data/index/write.lock
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/dspace/solr/statistics-2016/data/index/write.lock
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/dspace/solr/statistics-2017/data/index/write.lock
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/dspace/solr/statistics-2018/data/index/write.lock
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# find /dspace/solr/statistics* -iname "*.lock" -print -delete
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# systemctl start tomcat7
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</code></pre></li>
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<li><p>But it still didn’t work!</p></li>
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<li><p>I stopped Tomcat, deleted the old locks, and will try to use the “simple” lock file type in <code>solr/statistics/conf/solrconfig.xml</code>:</p>
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<pre><code><lockType>${solr.lock.type:simple}</lockType>
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</code></pre></li>
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<li><p>And after restarting Tomcat it still doesn’t work</p></li>
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<li><p>Now I’ll try going back to “native” locking with <code>unlockAtStartup</code>:</p>
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<pre><code><unlockOnStartup>true</unlockOnStartup>
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</code></pre></li>
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<li><p>Now the cores seem to load, but I still see an error in the Solr Admin UI and I still can’t access any stats before 2018</p></li>
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<li><p>I filed an <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685">issue with Atmire</a>, so let’s see if they can help</p></li>
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<li><p>And since I’m annoyed and it’s been a few months, I’m going to move the JVM heap settings that I’ve been testing on DSpace Test to CGSpace</p></li>
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<li><p>The old ones were:</p>
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<pre><code>-Djava.awt.headless=true -Xms8192m -Xmx8192m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=5400 -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false
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</code></pre></li>
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<li><p>And the new ones come from Solr 4.10.x’s startup scripts:</p>
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<pre><code>-Djava.awt.headless=true
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-Xms8192m -Xmx8192m
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-Dfile.encoding=UTF-8
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-XX:NewRatio=3
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-XX:SurvivorRatio=4
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-XX:TargetSurvivorRatio=90
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-XX:MaxTenuringThreshold=8
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-XX:+UseConcMarkSweepGC
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-XX:+UseParNewGC
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-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4
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-XX:+CMSScavengeBeforeRemark
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-XX:PretenureSizeThreshold=64m
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-XX:+UseCMSInitiatingOccupancyOnly
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-XX:CMSInitiatingOccupancyFraction=50
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-XX:CMSMaxAbortablePrecleanTime=6000
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-XX:+CMSParallelRemarkEnabled
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-XX:+ParallelRefProcEnabled
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-Dcom.sun.management.jmxremote
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-Dcom.sun.management.jmxremote.port=1337
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-Dcom.sun.management.jmxremote.ssl=false
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-Dcom.sun.management.jmxremote.authenticate=false
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</code></pre></li>
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</ul>
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<h2 id="2019-07-02">2019-07-02</h2>
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<ul>
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<li><p>Help upload twenty-seven posters from the 2019-05 Sharefair to CGSpace</p>
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<ul>
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<li><p>Sisay had already done the SAFBundle so I did some minor corrections to and uploaded them to a temporary collection so I could check them in OpenRefine:</p>
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<pre><code>$ sed -i 's/CC-BY 4.0/CC-BY-4.0/' item_*/dublin_core.xml
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$ echo "10568/101992" >> item_*/collections
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$ dspace import -a -e me@cgiar.org -m 2019-07-02-Sharefair.map -s /tmp/Sharefair_mapped
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</code></pre></li>
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</ul></li>
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<li><p>I noticed that all twenty-seven items had double dates like “2019-05||2019-05” so I fixed those, but the rest of the metadata looked good so I unmapped them from the temporary collection</p></li>
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<li><p>Finish looking at the fifty-six AfricaRice items and upload them to CGSpace:</p>
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<pre><code>$ dspace import -a -e me@cgiar.org -m 2019-07-02-AfricaRice-11to73.map -s /tmp/SimpleArchiveFormat
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</code></pre></li>
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<li><p>Peter pointed out that the Sharefair dates I fixed were not actually fixed</p>
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<ul>
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<li>It seems there is a bug that causes DSpace to not detect changes if the values are the same like “2019-05||2019-05” and you try to remove one</li>
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<li>To get it to work I had to change some of them to 2019-01, then remove them</li>
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</ul></li>
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</ul>
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<h2 id="2019-07-03">2019-07-03</h2>
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<ul>
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<li>Atmire responded about the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=685">Solr issue</a> and said they would be willing to help</li>
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</ul>
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<h2 id="2019-07-04">2019-07-04</h2>
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<ul>
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<li><p>Maria Garruccio sent me some new ORCID identifiers for Bioversity authors</p>
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<ul>
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<li><p>I combined them with our existing list and then used my <code>resolve-orcids.py</code> script to update the names from ORCID.org:</p>
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<pre><code>$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/new-bioversity-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2019-07-04-orcid-ids.txt
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$ ./resolve-orcids.py -i /tmp/2019-07-04-orcid-ids.txt -o 2019-07-04-orcid-names.txt -d
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</code></pre></li>
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</ul></li>
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<li><p>Send and merge a pull request for the new ORCID identifiers (<a href="https://github.com/ilri/DSpace/pull/428">#428</a>)</p></li>
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<li><p>I created a CSV with some ORCID identifiers that I had seen change so I could update any existing ones in the databse:</p>
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<pre><code>cg.creator.id,correct
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"Marius Ekué: 0000-0002-5829-6321","Marius R.M. Ekué: 0000-0002-5829-6321"
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"Mwungu: 0000-0001-6181-8445","Chris Miyinzi Mwungu: 0000-0001-6181-8445"
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"Mwungu: 0000-0003-1658-287X","Chris Miyinzi Mwungu: 0000-0003-1658-287X"
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</code></pre></li>
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<li><p>But when I ran <code>fix-metadata-values.py</code> I didn’t see any changes:</p>
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<pre><code>$ ./fix-metadata-values.py -i 2019-07-04-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d
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</code></pre></li>
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</ul>
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<h2 id="2019-07-06">2019-07-06</h2>
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<ul>
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<li>Send a reminder to Marie about my notes on the <a href="https://github.com/AgriculturalSemantics/cg-core/issues/2">CG Core v2 issue I created two weeks ago</a></li>
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</ul>
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<h2 id="2019-07-08">2019-07-08</h2>
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<ul>
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<li>Communicate with Atmire about the Solr statistics cores issue
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<ul>
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<li>I suspect we might need to get more disk space on DSpace Test so we can try to replicate the production environment more closely</li>
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</ul></li>
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<li>Meeting with AgroKnow and CTA about their new ICT Update story telling thing
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<ul>
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<li>AgroKnow has developed a React application to display tag clouds based on harvesting metadata and full text from CGSpace items</li>
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<li>We discussed how to host it technically, perhaps we purchase a server to run it on and just give AgroKnow guys access</li>
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</ul></li>
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<li><p>Playing with the idea of using <a href="https://github.com/BurntSushi/xsv">xsv</a> to do some basic batch quality checks on CSVs, for example to find items that might be duplicates if they have the same DOI or title:</p>
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<pre><code>$ xsv frequency --select cg.identifier.doi --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E ',1'
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field,value,count
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cg.identifier.doi,https://doi.org/10.1016/j.agwat.2018.06.018,2
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$ xsv frequency --select dc.title --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E ',1'
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field,value,count
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dc.title,Reference evapotranspiration prediction using hybridized fuzzy model with firefly algorithm: Regional case study in Burkina Faso,2
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</code></pre></li>
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<li><p>Or perhaps if DOIs are valid or not (having doi.org in the URL):</p>
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<pre><code>$ xsv frequency --select cg.identifier.doi --no-nulls cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v -E 'doi.org'
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field,value,count
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cg.identifier.doi,https://hdl.handle.net/10520/EJC-1236ac700f,1
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</code></pre></li>
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<li><p>Or perhaps items with invalid ISSNs (according to the <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number#Code_format">ISSN code format</a>):</p>
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<pre><code>$ xsv select dc.identifier.issn cgspace_metadata_africaRice-11to73_ay_id.csv | grep -v '"' | grep -v -E '^[0-9]{4}-[0-9]{3}[0-9xX]$'
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dc.identifier.issn
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978-3-319-71997-9
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978-3-319-71997-9
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978-3-319-71997-9
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978-3-319-58789-9
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2320-7035
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2593-9173
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</code></pre></li>
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</ul>
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<h2 id="2019-07-09">2019-07-09</h2>
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<ul>
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<li>Thinking about data cleaning automation again and found some resources about Python and Pandas:
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<ul>
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<li><a href="https://realpython.com/python-data-cleaning-numpy-pandas/">https://realpython.com/python-data-cleaning-numpy-pandas/</a></li>
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<li><a href="https://mode.com/blog/python-data-cleaning-libraries">https://mode.com/blog/python-data-cleaning-libraries</a></li>
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</ul></li>
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</ul>
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<h2 id="2019-07-11">2019-07-11</h2>
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<ul>
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<li>Skype call with Marie Angelique about CG Core v2
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<ul>
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<li>We discussed my comments and suggestions from last week</li>
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<li>One comment she had was that we should try to move our center-specific subjects into <code>DCTERMS.subject</code> and normalize them against AGROVOC</li>
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<li>I updated my <a href="https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409">gist about CGSpace metadata changes</a></li>
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</ul></li>
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<li>Skype call with Jane Poole to discuss OpenRXV/AReS Phase II TORs
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<ul>
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<li>I need to follow up with Moayad about the reporting functionality</li>
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<li>Also, I need to email Harrison my notes on the CG Core v2 stuff</li>
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<li>Also, Jane asked me to check the Data Portal to see which email address requests for confidential data are going</li>
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</ul></li>
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<li>Yesterday Theirry from CTA asked me about an error he was getting while submitting an item on CGSpace: “Unable to load Submission Information, since WorkspaceID (ID:S106658) is not a valid in-process submission.”</li>
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<li><p>I looked in the DSpace logs and found this right around the time of the screenshot he sent me:</p>
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<pre><code>2019-07-10 11:50:27,433 INFO org.dspace.submit.step.CompleteStep @ lewyllie@cta.int:session_id=A920730003BCAECE8A3B31DCDE11A97E:submission_complete:Completed submission with id=106658
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</code></pre></li>
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<li><p>I’m assuming something happened in his browser (like a refresh) after the item was submitted…</p></li>
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</ul>
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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/2019-07/">July, 2019</a></li>
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<li><a href="/cgspace-notes/posts/">Posts</a></li>
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<li><a href="/cgspace-notes/2019-06/">June, 2019</a></li>
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<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
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<li><a href="/cgspace-notes/2019-04/">April, 2019</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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<footer class="blog-footer">
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<p>
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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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