mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-26 08:28:18 +01:00
423 lines
18 KiB
HTML
423 lines
18 KiB
HTML
<!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’ve spent at least fifty hours to process the statistics and statistics-2019 core… 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" />
|
|
<meta property="article:modified_time" content="2020-11-13T09:22:18+02:00" />
|
|
|
|
<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’ve spent at least fifty hours to process the statistics and statistics-2019 core… wow.
|
|
|
|
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.78.1" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "November, 2020",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2020-11/",
|
|
"wordCount": "1565",
|
|
"datePublished": "2020-11-01T13:11:54+02:00",
|
|
"dateModified": "2020-11-13T09:22:18+02:00",
|
|
"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> <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’ve spent at least fifty hours to process the statistics and statistics-2019 core… 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’s default result set size of 10)</li>
|
|
<li>Invalid share link</li>
|
|
<li>Missing “https://” 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…
|
|
<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 “Data Paper” to types on CGSpace</li>
|
|
<li>Add “SCALING CLIMATE-SMART AGRICULTURE” to CCAFS subjects on CGSpace</li>
|
|
<li>Add “ANDEAN ROOTS AND TUBERS” 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’t have any statistics showing for years before 2020, but all cores are loaded successfully in Solr Admin UI… 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… perhaps a threading issue?
|
|
<ul>
|
|
<li>The only thing I can think of is the <code>acceptorThreadCount</code> parameter in Tomcat’s server.xml, which has been set to 2 since 2018-01 (we started sharding the Solr statistics cores in 2019-01 and that’s when this problem arose)</li>
|
|
<li>I will try reducing that to 1</li>
|
|
<li>Wow, now it’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… 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>
|
|
<h2 id="2020-11-11">2020-11-11</h2>
|
|
<ul>
|
|
<li>Atmire responded with a quote for the work to fix the duplicate owningComm, etc in our Solr data
|
|
<ul>
|
|
<li>I told them to proceed, as it’s within our budget of credits</li>
|
|
<li>They will write a processor for DSpace 6 to remove the duplicates</li>
|
|
</ul>
|
|
</li>
|
|
<li>I did some tests to add a usage statistics chart to the item views on DSpace Test
|
|
<ul>
|
|
<li>It is inspired by Salem’s work on WorldFish’s repository, and it hits the dspace-statistics-api for the current item and displays a graph</li>
|
|
<li>I got it working very easily for all-time statistics with Chart.js, but I think I will need to use Highcharts or something else because Chart.js is HTML5 canvas and doesn’t allow theming via CSS (so our Bootstrap brand colors for each theme won’t work)
|
|
<ul>
|
|
<li>Hmm, Highcharts is not licensed under and open source license so I will not use it</li>
|
|
<li>Perhaps I’ll use Chartist with the popover plugin…</li>
|
|
</ul>
|
|
</li>
|
|
<li>I think I’ll pursue this after the DSpace 6 upgrade…</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-11-12">2020-11-12</h2>
|
|
<ul>
|
|
<li>I was looking at Solr again trying to find a way to get community and collection stats by faceting on <code>owningComm</code> and <code>owningColl</code> and it seems to work actually
|
|
<ul>
|
|
<li>The duplicated values in the multi-value fields don’t seem to affect the counts, as I had thought previously (though we should still get rid of them)</li>
|
|
<li>One major difference between the raw numbers I was looking at and Atmire’s numbers is that Atmire’s code filters “Internal” IP addresses…</li>
|
|
<li>Also, instead of doing <code>isBot:false</code> I think I should do <code>-isBot:true</code> because it’s not a given that all documents will have this field and have it false, but we can definitely exclude the ones that have it as true</li>
|
|
</ul>
|
|
</li>
|
|
<li>First we get the total number of communities with stats (using calcdistinct):</li>
|
|
</ul>
|
|
<pre><code>facet=true&facet.field=owningComm&facet.mincount=1&facet.limit=1&facet.offset=0&stats=true&stats.field=owningComm&stats.calcdistinct=true&shards=http://localhost:8081/solr/statistics,http://localhost:8081/solr/statistics-2019,http://localhost:8081/solr/statistics-2018,http://localhost:8081/solr/statistics-2017,http://localhost:8081/solr/statistics-2016,http://localhost:8081/solr/statistics-2015,http://localhost:8081/solr/statistics-2014,http://localhost:8081/solr/statistics-2013,http://localhost:8081/solr/statistics-2012,http://localhost:8081/solr/statistics-2011,http://localhost:8081/solr/statistics-2010
|
|
</code></pre><ul>
|
|
<li>Then get stats themselves, iterating 100 items at a time with limit and offset:</li>
|
|
</ul>
|
|
<pre><code>facet=true&facet.field=owningComm&facet.mincount=1&facet.limit=100&facet.offset=0&shards=http://localhost:8081/solr/statistics,http://localhost:8081/solr/statistics-2019,http://localhost:8081/solr/statistics-2018,http://localhost:8081/solr/statistics-2017,http://localhost:8081/solr/statistics-2016,http://localhost:8081/solr/statistics-2015,http://localhost:8081/solr/statistics-2014,http://localhost:8081/solr/statistics-2013,http://localhost:8081/solr/statistics-2012,http://localhost:8081/solr/statistics-2011,http://localhost:8081/solr/statistics-2010
|
|
</code></pre><ul>
|
|
<li>I was surprised to see 10,000,000 docs with <code>isBot:true</code> when I was testing on DSpace Test…
|
|
<ul>
|
|
<li>This has got to be a mistake of some kind, as I see 4 million in 2014 that are from <code>dns:localhost.</code>, perhaps that’s when we didn’t have useProxies set up correctly?</li>
|
|
<li>I don’t see the same thing on CGSpace… I wonder what happened?</li>
|
|
<li>Perhaps they got re-tagged during the DSpace 6 upgrade, somehow during the Solr migration? Hmmmmm. Definitely have to be careful with <code>isBot:true</code> in the future and not automatically purge these!!!</li>
|
|
</ul>
|
|
</li>
|
|
<li>I noticed 120,000+ hits from monit, FeedBurner, and Blackboard Safeassign in 2014, 2015, 2016, 2017, etc…
|
|
<ul>
|
|
<li>I hadn’t seen monit before, but the others are already in DSpace’s spider agents lists for some time so probably only appear in older stats cores</li>
|
|
<li>The issue with purging these using <code>check-spider-hits.sh</code> is that it can’t do case-insensitive regexes and some metacharacters like <code>\s</code> don’t work so I added case-sensitive patterns to a local agents file and purged them with the script</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-11-15">2020-11-15</h2>
|
|
<ul>
|
|
<li>Upgrade CGSpace to DSpace 6.3
|
|
<ul>
|
|
<li>First build, update, and migrate the database:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>$ dspace cleanup -v
|
|
$ git checkout origin/6_x-dev-atmire-modules
|
|
$ npm install -g yarn
|
|
$ chrt -b 0 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2,\!dspace-jspui clean package
|
|
$ sudo su - postgres
|
|
$ psql dspace -c 'CREATE EXTENSION pgcrypto;'
|
|
$ psql dspace -c "DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');"
|
|
$ exit
|
|
$ rm -rf /home/cgspace/config/spring
|
|
$ ant update
|
|
$ dspace database info
|
|
$ dspace database migrate
|
|
$ sudo systemctl start tomcat7
|
|
</code></pre><ul>
|
|
<li>After starting Tomcat DSpace should start up OK and begin Discovery indexing, but I want to also upgrade from PostgreSQL 9.6 to 10
|
|
<ul>
|
|
<li>I installed and configured PostgreSQL 10 using the Ansible playbooks, then migrated the database manually:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code># systemctl stop tomcat7
|
|
# pg_ctlcluster 9.6 main stop
|
|
# tar -cvzpf var-lib-postgresql-9.6.tar.gz /var/lib/postgresql/9.6
|
|
# tar -cvzpf etc-postgresql-9.6.tar.gz /etc/postgresql/9.6
|
|
# pg_ctlcluster 10 main stop
|
|
# pg_dropcluster 10 main
|
|
# pg_upgradecluster 9.6 main
|
|
# pg_dropcluster 9.6 main
|
|
# systemctl start postgresql
|
|
# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r
|
|
</code></pre><ul>
|
|
<li>Then I ran all system updates and rebooted the server…</li>
|
|
<li>After the server came back up I re-ran the Ansible playbook to make sure all configs and services were updated</li>
|
|
<li>I disabled the dspace-statistsics-api for now because it won’t work until I migrate all the Solr statistics anyways</li>
|
|
<li>Start a full Discovery re-indexing:</li>
|
|
</ul>
|
|
<pre><code>$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
|
</code></pre><ul>
|
|
<li>I updated all the Ansible infrastructure and DSpace branches to be the DSpace 6 ones</li>
|
|
<li>I will wait until the Discovery indexing is finished to start doing the Solr statistics migration</li>
|
|
</ul>
|
|
<!-- raw HTML omitted -->
|
|
|
|
|
|
|
|
|
|
|
|
</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>
|