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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/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></h2>
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<p class="blog-post-meta">
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<time datetime="2020-11-15T13:27:35+02:00">Sun Nov 15, 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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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/migration/" rel="tag">Migration</a>
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</p>
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</header>
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<p>Notes about the DSpace 6 upgrade on CGSpace in 2020-11.</p>
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<ul>
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<li><a href="#re-import-oai-with-clean-index">Re-import OAI with clean index</a></li>
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<li><a href="#processing-solr-statistics-with-solr-upgrade-statistics-6x">Processing Solr statistics with solr-upgrade-statistics-6x</a>
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<ul>
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<li><a href="#statistics">Current year’s statistics core</a></li>
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<li><a href="#statistics-2019">statistics-2019 core</a></li>
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<li><a href="#statistics-2018">statistics-2018 core</a></li>
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<li><a href="#statistics-2017">statistics-2017 core</a></li>
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<li><a href="#statistics-2016">statistics-2016 core</a></li>
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<li><a href="#statistics-2015">statistics-2015 core</a></li>
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<li><a href="#statistics-2014">statistics-2014 core</a></li>
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<li><a href="#statistics-2013">statistics-2013 core</a></li>
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<li><a href="#statistics-2012">statistics-2013 core</a></li>
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<li><a href="#statistics-2011">statistics-2013 core</a></li>
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<li><a href="#statistics-2010">statistics-2013 core</a></li>
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</ul>
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</li>
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<li><a href="processing-solr-statistics-with-atomicstatisticsupdatecli">Processing Solr statistics with AtomicStatisticsUpdateCLI</a></li>
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</ul>
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<h3 id="re-import-oai-with-clean-index">Re-import OAI with clean index</h3>
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<p>After the upgrade is complete, re-index all items into OAI with a clean index:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m"
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$ dspace oai -c import
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</code></pre><p>The process ran out of memory several times so I had to keep trying again with more JVM heap memory.</p>
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<h3 id="processing-solr-statistics-with-solr-upgrade-statistics-6x">Processing Solr Statistics With solr-upgrade-statistics-6x</h3>
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<p>After the main upgrade process was finished and DSpace was running I started processing the Solr statistics with <code>solr-upgrade-statistics-6x</code> to migrate all IDs to UUIDs.</p>
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<h2 id="statistics">statistics</h2>
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<p>First process the current year’s statistics core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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3,817,407 Bistream View
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1,693,443 Item View
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105,974 Collection View
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62,383 Community View
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163,192 Community Search
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162,581 Collection Search
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470,288 Unexpected Type & Full Site
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--------------------------------------
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6,475,268 TOTAL
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=================================================================
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</code></pre><p>After several rounds of processing it finished. Here are some statistics about unmigrated documents:</p>
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<ul>
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<li>227,000: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>471,000: <code>id:/.+-unmigrated/</code></li>
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<li>698,000: <code>*:* NOT id:/.{36}/</code></li>
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<li>Majority are <code>type: 5</code> (aka SITE, according to <code>Constants.java</code>) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2019">statistics-2019</h2>
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<p>Processing the statistics-2019 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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5,569,344 Bistream View
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2,179,105 Item View
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117,194 Community View
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104,091 Collection View
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774,138 Community Search
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568,347 Collection Search
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1,482,620 Unexpected Type & Full Site
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--------------------------------------
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10,794,839 TOTAL
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=================================================================
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</code></pre><p>After several rounds of processing it finished. Here are some statistics about unmigrated documents:</p>
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<ul>
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<li>2,690,309: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>1,494,587: <code>id:/.+-unmigrated/</code></li>
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<li>4,184,896: <code>*:* NOT id:/.{36}/</code></li>
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<li>4,172,929 are <code>type: 5</code> (aka SITE) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2019/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2018">statistics-2018</h2>
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<p>Processing the statistics-2018 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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3,561,532 Bistream View
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1,129,326 Item View
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97,401 Community View
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63,508 Collection View
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207,827 Community Search
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43,752 Collection Search
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457,820 Unexpected Type & Full Site
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--------------------------------------
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5,561,166 TOTAL
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=================================================================
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</code></pre><p>After some time I got an error about Java heap space so I increased the JVM memory and restarted processing:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx4096m'
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$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
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</code></pre><p>Eventually the processing finished. Here are some statistics about unmigrated documents:</p>
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<ul>
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<li>365,473: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>546,955: <code>id:/.+-unmigrated/</code></li>
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<li>923,158: <code>*:* NOT id:/.{36}/</code></li>
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<li>823,293: are <code>type: 5</code> so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2018/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2017">statistics-2017</h2>
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<p>Processing the statistics-2017 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2017
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,529,208 Bistream View
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1,618,717 Item View
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144,945 Community View
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74,249 Collection View
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479,647 Community Search
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114,658 Collection Search
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852,215 Unexpected Type & Full Site
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--------------------------------------
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5,813,639 TOTAL
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=================================================================
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</code></pre><p>Eventually the processing finished. Here are some statistics about unmigrated documents:</p>
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<ul>
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<li>808,309: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>893,868: <code>id:/.+-unmigrated/</code></li>
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<li>1,702,177: <code>*:* NOT id:/.{36}/</code></li>
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<li>1,660,524 are <code>type: 5</code> (SITE) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2017/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2016">statistics-2016</h2>
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<p>Processing the statistics-2016 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2016
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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1,765,924 Bistream View
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1,151,575 Item View
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187,110 Community View
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51,204 Collection View
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347,382 Community Search
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66,605 Collection Search
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620,298 Unexpected Type & Full Site
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--------------------------------------
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4,190,098 TOTAL
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=================================================================
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</code></pre><ul>
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<li>849,408: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>627,747: <code>id:/.+-unmigrated/</code></li>
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<li>1,477,155: <code>*:* NOT id:/.{36}/</code></li>
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<li>1,469,706 are <code>type: 5</code> (SITE) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2016/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2015">statistics-2015</h2>
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<p>Processing the statistics-2015 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2015
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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990,916 Bistream View
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506,070 Item View
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116,153 Community View
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33,282 Collection View
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21,062 Community Search
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10,788 Collection Search
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52,107 Unexpected Type & Full Site
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--------------------------------------
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1,730,378 TOTAL
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=================================================================
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</code></pre><p>Summary of stats after processing:</p>
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<ul>
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<li>195,293: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>67,146: <code>id:/.+-unmigrated/</code></li>
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<li>262,439: <code>*:* NOT id:/.{36}/</code></li>
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<li>247,400 are <code>type: 5</code> (SITE) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2015/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2014">statistics-2014</h2>
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<p>Processing the statistics-2014 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2014
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,381,603 Item View
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1,323,357 Bistream View
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501,545 Community View
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247,805 Collection View
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250 Collection Search
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188 Community Search
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50 Item Search
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10,918 Unexpected Type & Full Site
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--------------------------------------
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4,465,716 TOTAL
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=================================================================
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</code></pre><p>Summary of unmigrated documents after processing:</p>
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<ul>
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<li>182,131: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>39,947: <code>id:/.+-unmigrated/</code></li>
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<li>222,078: <code>*:* NOT id:/.{36}/</code></li>
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<li>188,791 are <code>type: 5</code> (SITE) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2014/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2013">statistics-2013</h2>
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<p>Processing the statistics-2013 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2013
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,352,124 Item View
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1,117,676 Bistream View
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575,711 Community View
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171,639 Collection View
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248 Item Search
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7 Collection Search
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5 Community Search
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1,452 Unexpected Type & Full Site
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--------------------------------------
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4,218,862 TOTAL
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=================================================================
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</code></pre><p>Summary of unmigrated docs after processing:</p>
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<ul>
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<li>2,548 : <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>29,772: <code>id:/.+-unmigrated/</code></li>
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<li>32,320: <code>*:* NOT id:/.{36}/</code></li>
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<li>15,691 are <code>type: 5</code> (SITE) so we can purge them:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2013/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2012">statistics-2012</h2>
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<p>Processing the statistics-2012 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2012
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
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2,229,332 Item View
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913,577 Bistream View
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215,577 Collection View
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104,734 Community View
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--------------------------------------
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3,463,220 TOTAL
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=================================================================
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</code></pre><p>Summary of unmigrated docs after processing:</p>
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<ul>
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<li>0: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
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<li>33,161: <code>id:/.+-unmigrated/</code></li>
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<li>33,161: <code>*:* NOT id:/.{36}/</code></li>
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<li>33,161 are <code>type: 3</code> (COLLECTION), which is different than I’ve seen previously… but I suppose I still have to purge them because there will be errors in the Atmire modules otherwise:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2012/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
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</code></pre><h2 id="statistics-2011">statistics-2011</h2>
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<p>Processing the statistics-2011 core:</p>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2011
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...
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=================================================================
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*** Statistics Records with Legacy Id ***
|
|
|
|
904,896 Item View
|
|
385,789 Bistream View
|
|
154,356 Collection View
|
|
62,978 Community View
|
|
--------------------------------------
|
|
1,508,019 TOTAL
|
|
=================================================================
|
|
</code></pre><p>Summary of unmigrated docs after processing:</p>
|
|
<ul>
|
|
<li>0: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
|
|
<li>17,551: <code>id:/.+-unmigrated/</code></li>
|
|
<li>17,551: <code>*:* NOT id:/.{36}/</code></li>
|
|
<li>12,116 are <code>type: 3</code> (COLLECTION), which is different than I’ve seen previously… but I suppose I still have to purge them because there will be errors in the Atmire modules otherwise:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2011/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
|
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</code></pre><h2 id="statistics-2010">statistics-2010</h2>
|
|
<p>Processing the statistics-2010 core:</p>
|
|
<pre tabindex="0"><code class="language-console" data-lang="console">$ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2010
|
|
...
|
|
=================================================================
|
|
*** Statistics Records with Legacy Id ***
|
|
|
|
26,067 Item View
|
|
15,615 Bistream View
|
|
4,116 Collection View
|
|
1,094 Community View
|
|
--------------------------------------
|
|
46,892 TOTAL
|
|
=================================================================
|
|
</code></pre><p>Summary of unmigrated docs after processing:</p>
|
|
<ul>
|
|
<li>0: <code>(*:* NOT id:/.{36}/) AND (*:* NOT id:/.+-unmigrated/)</code></li>
|
|
<li>1,012: <code>id:/.+-unmigrated/</code></li>
|
|
<li>1,012: <code>*:* NOT id:/.{36}/</code></li>
|
|
<li>654 are <code>type: 3</code> (COLLECTION), which is different than I’ve seen previously… but I suppose I still have to purge them because there will be errors in the Atmire modules otherwise:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>*:* NOT id:/.{36}/</query></delete>"
|
|
</code></pre><h3 id="processing-solr-statistics-with-atomicstatisticsupdatecli">Processing Solr statistics with AtomicStatisticsUpdateCLI</h3>
|
|
<p>On 2020-11-18 I finished processing the Solr statistics with solr-upgrade-statistics-6x and I started processing them with AtomicStatisticsUpdateCLI.</p>
|
|
<h2 id="statistics-1">statistics</h2>
|
|
<p>First the current year’s statistics core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics
|
|
</code></pre><p>It took ~38 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2019-1">statistics-2019</h2>
|
|
<p>The statistics-2019 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2019
|
|
</code></pre><p>It took ~32 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2018-1">statistics-2018</h2>
|
|
<p>The statistics-2018 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2018
|
|
</code></pre><p>It took ~28 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2017-1">statistics-2017</h2>
|
|
<p>The statistics-2017 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2017
|
|
</code></pre><p>It took ~24 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2016-1">statistics-2016</h2>
|
|
<p>The statistics-2016 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2016
|
|
</code></pre><p>It took ~20 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2015-1">statistics-2015</h2>
|
|
<p>The statistics-2015 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
|
|
</code></pre><p>It took ~21 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2014-1">statistics-2014</h2>
|
|
<p>The statistics-2014 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2014
|
|
</code></pre><p>It took ~12 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2013-1">statistics-2013</h2>
|
|
<p>The statistics-2013 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2013
|
|
</code></pre><p>It took ~3 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2012-1">statistics-2012</h2>
|
|
<p>The statistics-2012 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2012
|
|
</code></pre><p>It took ~2 hours to finish processing this core.</p>
|
|
<h2 id="statistics-2011-1">statistics-2011</h2>
|
|
<p>The statistics-2011 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2011
|
|
</code></pre><p>It took 1 hour to finish processing this core.</p>
|
|
<h2 id="statistics-2010-1">statistics-2010</h2>
|
|
<p>The statistics-2010 core, in 12-hour batches:</p>
|
|
<pre tabindex="0"><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2010
|
|
</code></pre><p>It took five minutes to finish processing this core.</p>
|
|
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</article>
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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/2021-10/">October, 2021</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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