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Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
So far we&rsquo;ve spent at least fifty hours to process the statistics and statistics-2019 core&hellip; wow.
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Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
So far we&rsquo;ve spent at least fifty hours to process the statistics and statistics-2019 core&hellip; wow.
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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/2020-11/">November, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-11-01T13:11:54+02:00">Sun Nov 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2020-11-01">2020-11-01</h2>
<ul>
<li>Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
<ul>
<li>So far we&rsquo;ve spent at least fifty hours to process the statistics and statistics-2019 core&hellip; wow.</li>
</ul>
</li>
</ul>
<h2 id="2020-11-02">2020-11-02</h2>
<ul>
<li>Talk to Moayad and fix a few issues on OpenRXV:
<ul>
<li>Incorrect views and downloads (caused by Elasticsearch&rsquo;s default result set size of 10)</li>
<li>Invalid share link</li>
<li>Missing &ldquo;https://&rdquo; for Handles in the Simple Excel report (caused by using the <code>handle</code> instead of the <code>uri</code>)</li>
<li>Sorting the list of items by views</li>
</ul>
</li>
<li>I resumed the processing of the statistics-2018 Solr core after it spent 20 hours to get to 60%</li>
</ul>
<h2 id="2020-11-04">2020-11-04</h2>
<ul>
<li>After 29 hours the statistics-2017 core finished processing so I started the statistics-2016 core on DSpace Test</li>
</ul>
<h2 id="2020-11-05">2020-11-05</h2>
<ul>
<li>Peter sent me corrections and deletions for the author affiliations
<ul>
<li>I quickly proofed them for UTF-8 issues in OpenRefine and csv-metadata-quality and then tested them locally and then applied them on CGSpace:</li>
</ul>
</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i 2020-11-05-fix-862-affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -t 'correct' -m 211
$ ./delete-metadata-values.py -i 2020-11-05-delete-29-affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211
</code></pre><ul>
<li>Then I started a Discovery re-index on CGSpace:</li>
</ul>
<pre><code>$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
real 92m24.993s
user 8m11.858s
sys 2m26.931s
</code></pre><h2 id="2020-11-06">2020-11-06</h2>
<ul>
<li>Restart the AtomicStatisticsUpdateCLI processing of the statistics-2016 core on DSpace Test after 20 hours&hellip;
<ul>
<li>This phase finished after five hours so I started it on the statistics-2015 core</li>
</ul>
</li>
</ul>
<h2 id="2020-11-07">2020-11-07</h2>
<ul>
<li>Atmire responded about the issue with duplicate values in owningComm and containerCommunity etc
<ul>
<li>I told them to please look into it and use some of our credits if need be</li>
</ul>
</li>
<li>The statistics-2015 core finished after 20 hours so I started the statistics-2014 core</li>
</ul>
<h2 id="2020-11-08">2020-11-08</h2>
<ul>
<li>Add &ldquo;Data Paper&rdquo; to types on CGSpace</li>
<li>Add &ldquo;SCALING CLIMATE-SMART AGRICULTURE&rdquo; to CCAFS subjects on CGSpace</li>
<li>Add &ldquo;ANDEAN ROOTS AND TUBERS&rdquo; to CIP subjects on CGSpace</li>
<li>Add CGIAR System subjects to Discovery sidebar facets on CGSpace
<ul>
<li>Also add the System subject to item view on CGSpace</li>
</ul>
</li>
<li>The statistics-2014 core finished processing after five hours, so I started processing the statistics-2013 core on DSpace Test</li>
<li>Since I was going to restart CGSpace and update the Discovery indexes anyways I decided to check for any straggling upper case AGROVOC entries and lower case them:</li>
</ul>
<pre><code>dspace=# BEGIN;
dspace=# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE resource_type_id=2 AND metadata_field_id=57 AND text_value ~ '[[:upper:]]';
UPDATE 164
dspace=# COMMIT;
</code></pre><ul>
<li>Run system updates on CGSpace (linode18) and reboot it
<ul>
<li>I had to restart Tomcat once after the machine started up to get all Solr statistics cores to load properly</li>
</ul>
</li>
<li>After about ten more hours the rest of the Solr statistics cores finished processing on DSpace Test and I started optimizing them in Solr admin UI</li>
</ul>
<h2 id="2020-11-10">2020-11-10</h2>
<ul>
<li>I am noticing that CGSpace doesn&rsquo;t have any statistics showing for years before 2020, but all cores are loaded successfully in Solr Admin UI&hellip; strange
<ul>
<li>I restarted Tomcat and I see in Solr Admin UI that the statistics-2015 core failed to load</li>
<li>Looking in the DSpace log I see:</li>
</ul>
</li>
</ul>
<pre><code>2020-11-10 08:43:59,634 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:43:59,687 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2018
2020-11-10 08:43:59,707 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:44:00,004 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,005 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,005 WARN org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2020-11-10 08:44:00,325 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2015
</code></pre><ul>
<li>Seems that the core gets probed twice&hellip; perhaps a threading issue?
<ul>
<li>The only thing I can think of is the <code>acceptorThreadCount</code> parameter in Tomcat&rsquo;s server.xml, which has been set to 2 since 2018-01 (we started sharding the Solr statistics cores in 2019-01 and that&rsquo;s when this problem arose)</li>
<li>I will try reducing that to 1</li>
<li>Wow, now it&rsquo;s even worse:</li>
</ul>
</li>
</ul>
<pre><code>2020-11-10 08:51:03,007 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2018
2020-11-10 08:51:03,008 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:51:03,137 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2018
2020-11-10 08:51:03,153 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2015
2020-11-10 08:51:03,289 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2015
2020-11-10 08:51:03,289 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2010
2020-11-10 08:51:03,475 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2010
2020-11-10 08:51:03,475 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2016
2020-11-10 08:51:03,730 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
2020-11-10 08:51:03,731 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2017
2020-11-10 08:51:03,992 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2017
2020-11-10 08:51:03,992 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2011
2020-11-10 08:51:04,178 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2011
2020-11-10 08:51:04,178 INFO org.dspace.statistics.SolrLogger @ Loading core with name: statistics-2012
</code></pre><ul>
<li>Could it be because we have two Tomcat connectors?
<ul>
<li>I restarted Tomcat a few more times before all cores loaded, and still there are no stats before 2020-01&hellip; hmmmmm</li>
</ul>
</li>
<li>I added a <a href="https://github.com/ilri/OpenRXV/commit/3816b9b3f3d9182d2ba1a899c1017c5895a59dee">lowercase formatter to OpenRXV</a> so that we can lowercase AGROVOC subjects during harvesting</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
<li><a href="/cgspace-notes/2020-10/">October, 2020</a></li>
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
<li><a href="/cgspace-notes/2020-07/">July, 2020</a></li>
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<h4>Links</h4>
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<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>
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