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<meta property="og:description" content="2020-12-01
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Atmire responded about the issue with duplicate data in our Solr statistics
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They noticed that some records in the statistics-2015 core haven’t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven’t migrated any of the records yet
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That’s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the cua_version field
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I started processing those (about 411,000 records):
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<meta name="twitter:title" content="December, 2020"/>
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<meta name="twitter:description" content="2020-12-01
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Atmire responded about the issue with duplicate data in our Solr statistics
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They noticed that some records in the statistics-2015 core haven’t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven’t migrated any of the records yet
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That’s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the cua_version field
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I started processing those (about 411,000 records):
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<title>December, 2020 | CGSpace Notes</title>
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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/2020-12/">December, 2020</a></h2>
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<time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</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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</p>
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</header>
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<h2 id="2020-12-01">2020-12-01</h2>
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<ul>
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<li>Atmire responded about the issue with duplicate data in our Solr statistics
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<ul>
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<li>They noticed that some records in the statistics-2015 core haven’t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven’t migrated any of the records yet</li>
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<li>That’s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
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<li>I started processing those (about 411,000 records):</li>
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</ul>
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</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
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</code></pre><ul>
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<li>AReS went down when the <code>renew-letsencrypt</code> service stopped the <code>angular_nginx</code> container in the pre-update hook and failed to bring it back up
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<ul>
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<li>I ran all system updates on the host and rebooted it and AReS came back up OK</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-12-02">2020-12-02</h2>
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<ul>
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<li>Udana emailed me yesterday to ask why the CGSpace usage statistics were showing “No Data”
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<ul>
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<li>I noticed a message in the Solr Admin UI that one of the statistics cores failed to load, but it is up and I can query it…</li>
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<li>Nevertheless, I restarted Tomcat a few times to see if all cores would come up without an error message, but had no success (despite that all cores ARE up and I can query them, <em>sigh</em>)</li>
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<li>I think I will move all the Solr yearly statistics back into the main statistics core</li>
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</ul>
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</li>
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<li>Start testing export/import of yearly Solr statistics data into the main statistics core on DSpace Test, for example:</li>
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</ul>
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<pre><code>$ ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
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$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
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$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:*</query></delete>"
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</code></pre><ul>
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<li>I deployed Tomcat 7.0.107 on DSpace Test (CGSpace is still Tomcat 7.0.104)</li>
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<li>I finished migrating all the statistics from the yearly shards back to the main core</li>
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</ul>
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<h2 id="2020-12-05">2020-12-05</h2>
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<ul>
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<li>I deleted all the yearly statistics shards and restarted Tomcat on DSpace Test (linode26)</li>
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</ul>
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<h2 id="2020-12-06">2020-12-06</h2>
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<ul>
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<li>Looking into the statistics on DSpace Test after I migrated them back to the main core
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<ul>
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<li>All stats are working as expected… indexing time for the DSpace Statistics API is the same… and I don’t even see a difference in the JVM or memory stats in Munin other than a minor jump last week when I was processing them</li>
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</ul>
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</li>
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<li>I will migrate them on CGSpace too I think
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<ul>
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<li>First I will start with the statistics-2010 and statistics-2015 cores because they were the ones that were failing to load recently (despite actually being available in Solr WTF)</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2020/12/solr-statistics-2010-failed.png" alt="Error message in Solr admin UI about the statistics-2010 core failing to load"></p>
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<ul>
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<li>First the 2010 core:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o statistics-2010.json -k uid
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$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a import -o statistics-2010.json -k uid
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$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:*</query></delete>"
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</code></pre><ul>
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<li>Judging by the DSpace logs all these cores had a problem starting up in the last month:</li>
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</ul>
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<pre><code class="language-console" data-lang="console"># grep -rsI "Unable to create core" [dspace]/log/dspace.log.2020-* | grep -o -E "statistics-[0-9]+" | sort | uniq -c
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24 statistics-2010
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24 statistics-2015
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18 statistics-2016
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6 statistics-2018
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</code></pre><ul>
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<li>The message is always this:</li>
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</ul>
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<pre><code>org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: Error CREATEing SolrCore 'statistics-2016': Unable to create core [statistics-2016] Caused by: Lock obtain timed out: NativeFSLock@/[dspace]/solr/statistics-2016/data/index/write.lock
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</code></pre><ul>
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<li>I will migrate all these cores and see if it makes a difference, then probably end up migrating all of them
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<ul>
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<li>I removed the statistics-2010, statistics-2015, statistics-2016, and statistics-2018 cores and restarted Tomcat and <em>all the statistics cores came up OK and the CUA statistics are OK</em>!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-12-07">2020-12-07</h2>
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<ul>
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<li>Run <code>dspace cleanup -v</code> on CGSpace to clean up deleted bitstreams</li>
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<li>Atmire sent a <a href="https://github.com/ilri/DSpace/pull/457">pull request</a> to address the duplicate owningComm and owningColl
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<ul>
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<li>Built and deployed it on DSpace Test but I am not sure how to run it yet</li>
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<li>I sent feedback to Atmire on their tracker: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=839</a></li>
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</ul>
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</li>
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<li>Abenet and Tezira are having issues with committing to the archive in their workflow
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<ul>
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<li>I looked at the server and indeed the locks and transactions are back up:</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2020/12/postgres_transactions_ALL-day.png" alt="PostgreSQL Transactions day">
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<img src="/cgspace-notes/2020/12/postgres_locks_ALL-day.png" alt="PostgreSQL Locks day">
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<img src="/cgspace-notes/2020/12/postgres_querylength_ALL-day.png" alt="PostgreSQL Locks day">
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<img src="/cgspace-notes/2020/12/postgres_connections_ALL-day.png" alt="PostgreSQL Connections day"></p>
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<ul>
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<li>There are apparently 1,700 locks right now:</li>
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</ul>
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<pre><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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1739
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</code></pre><h2 id="2020-12-08">2020-12-08</h2>
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<ul>
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<li>Atmire sent some instructions for using the DeduplicateValuesProcessor
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<ul>
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<li>I modified <code>atmire-cua-update.xml</code> as they instructed, but I get a million errors like this when I run AtomicStatisticsUpdateCLI with that configuration:</li>
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</ul>
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</li>
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</ul>
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<pre><code>Record uid: 64387815-d9a7-4605-8024-1c0a5c7520e0 couldn't be processed
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com.atmire.statistics.util.update.atomic.ProcessingException: something went wrong while processing record uid: 64387815-d9a7-4605-8024-1c0a5c7520e0, an error occured in the com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor
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at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:304)
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at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.processRecords(SourceFile:176)
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at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.performRun(SourceFile:161)
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at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.update(SourceFile:128)
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at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI.main(SourceFile:78)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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Caused by: java.lang.UnsupportedOperationException
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at org.apache.solr.common.SolrDocument$1.entrySet(SolrDocument.java:256)
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at java.util.HashMap.putMapEntries(HashMap.java:512)
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at java.util.HashMap.<init>(HashMap.java:490)
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at com.atmire.statistics.util.update.atomic.record.Record.getFieldValuesMap(SourceFile:86)
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at com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor.process(SourceFile:38)
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at com.atmire.statistics.util.update.atomic.processor.DeduplicateValuesProcessor.visit(SourceFile:34)
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at com.atmire.statistics.util.update.atomic.record.UsageRecord.accept(SourceFile:23)
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at com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdater.applyProcessors(SourceFile:301)
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... 10 more
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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/2020-12/">December, 2020</a></li>
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<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
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<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
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<li><a href="/cgspace-notes/2020-10/">October, 2020</a></li>
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<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
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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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