alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-05 14:53:02 +01:00
Code Issues Projects Releases Wiki Activity
b99114d8e4
cgspace-notes/docs/2020-11/index.html

322 lines
12 KiB
HTML
Raw Normal View History

Add notes for 2020-11
2020-11-04 19:41:19 +01:00
<!DOCTYPE html>
<html lang="en" >
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="November, 2020" />
<meta property="og:description" content="2020-11-01
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.
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-11/" />
<meta property="article:published_time" content="2020-11-01T13:11:54+02:00" />
Add notes for 2020-11-10
2020-11-10 16:00:02 +01:00
<meta property="article:modified_time" content="2020-11-08T15:03:02+02:00" />
Add notes for 2020-11
2020-11-04 19:41:19 +01:00
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="November, 2020"/>
<meta name="twitter:description" content="2020-11-01
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.
"/>
Add notes for 2020-11-07
2020-11-07 15:22:36 +01:00
<meta name="generator" content="Hugo 0.78.1" />
Add notes for 2020-11
2020-11-04 19:41:19 +01:00
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "BlogPosting",
"headline": "November, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-11/",
Add notes for 2020-11-10
2020-11-10 16:00:02 +01:00
"wordCount": "817",
Add notes for 2020-11
2020-11-04 19:41:19 +01:00
"datePublished": "2020-11-01T13:11:54+02:00",
Add notes for 2020-11-10
2020-11-10 16:00:02 +01:00
"dateModified": "2020-11-08T15:03:02+02:00",
Add notes for 2020-11
2020-11-04 19:41:19 +01:00
"author": {
"@type": "Person",
"name": "Alan Orth"
},
"keywords": "Notes"
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-11/">
<title>November, 2020 | CGSpace Notes</title>
<!-- combined, minified CSS -->
<link href="https://alanorth.github.io/cgspace-notes/css/style.6da5c906cc7a8fbb93f31cd2316c5dbe3f19ac4aa6bfb066f1243045b8f6061e.css" rel="stylesheet" integrity="sha256-baXJBsx6j7uT8xzSMWxdvj8ZrEqmv7Bm8SQwRbj2Bh4=" crossorigin="anonymous">
<!-- minified Font Awesome for SVG icons -->
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f3d2a1f5980bab30ddd0d8cadbd496475309fc48e2b1d052c5c09e6facffcb0f.js" integrity="sha256-89Kh9ZgLqzDd0NjK29SWR1MJ/EjisdBSxcCeb6z/yw8=" crossorigin="anonymous"></script>
<!-- RSS 2.0 feed -->
</head>
<body>
<div class="blog-masthead">
<div class="container">
<nav class="nav blog-nav">
<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
</nav>
</div>
</div>
<header class="blog-header">
<div class="container">
<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
</div>
</header>
<div class="container">
<div class="row">
<div class="col-sm-8 blog-main">
<article class="blog-post">
<header>
<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>
</p>
</header>
<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>
Add notes for 2020-11-05
2020-11-05 11:14:50 +01:00
<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
Update notes for 2020-11-05
2020-11-05 13:04:34 +01:00
real 92m24.993s
user 8m11.858s
sys 2m26.931s
Add notes for 2020-11-07
2020-11-07 15:22:36 +01:00
</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>
Add notes for 2020-11-08
2020-11-08 13:43:00 +01:00
<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>
Update notes for 2020-11-08
2020-11-08 14:03:02 +01:00
<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>
Add notes for 2020-11-10
2020-11-10 16:00:02 +01:00
<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>
Add notes for 2020-11-08
2020-11-08 13:43:00 +01:00
</ul>
Add notes for 2020-11-07
2020-11-07 15:22:36 +01:00
<!-- raw HTML omitted -->
Add notes for 2020-11
2020-11-04 19:41:19 +01:00
</article>
</div> <!-- /.blog-main -->
<aside class="col-sm-3 ml-auto blog-sidebar">
<section class="sidebar-module">
<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>
</ol>
</section>
<section class="sidebar-module">
<h4>Links</h4>
<ol class="list-unstyled">
<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>
</ol>
</section>
</aside>
</div> <!-- /.row -->
</div> <!-- /.container -->
<footer class="blog-footer">
<p dir="auto">
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
</p>
<p>
<a href="#">Back to top</a>
</p>
</footer>
</body>
</html>
Reference in New Issue Copy Permalink