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Add notes for 2018-01-19

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Alan Orth 2018-01-19 17:45:27 +02:00
parent 13d27d41f3
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45 changed files with 414 additions and 52 deletions
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11
content/post/2018-01.md
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@ -901,4 +901,15 @@ Jan 18 07:01:22 linode18 sudo[10812]: swebshet : TTY=pts/3 ; PWD=/home/swebshet
Jan 18 07:01:22 linode18 sudo[10812]: pam_unix(sudo:session): session opened for user root by swebshet(uid=0)
```
- I had to cancel the Discovery indexing and I'll have to re-try it another time when the server isn't so busy (it had already taken two hours and wasn't even close to being done)
- For now I've increased the Tomcat JVM heap from 5632 to 6144m, to give ~1GB of free memory over the average usage to hopefully account for spikes caused by load or background jobs
## 2018-01-19
- Linode alerted and said that the CPU load was 264% on CGSpace
- Start the Discovery indexing again:
```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
$ time schedtool -D -e ionice -c2 -n7 nice -n19 /home/cgspace.cgiar.org/bin/dspace index-discovery -b
```

2
public/2015-11/index.html
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@ -52,7 +52,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac
"/>
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2
public/2015-12/index.html
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@ -54,7 +54,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
"/>
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2
public/2016-01/index.html
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@ -44,7 +44,7 @@ Update GitHub wiki for documentation of maintenance tasks.
"/>
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2
public/2016-02/index.html
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@ -58,7 +58,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
"/>
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2
public/2016-03/index.html
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@ -44,7 +44,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
"/>
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2
public/2016-04/index.html
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@ -48,7 +48,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
"/>
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2
public/2016-05/index.html
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@ -52,7 +52,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
"/>
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2
public/2016-06/index.html
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@ -50,7 +50,7 @@ Working on second phase of metadata migration, looks like this will work for mov
"/>
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public/2016-07/index.html
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@ -66,7 +66,7 @@ In this case the select query was showing 95 results before the update
"/>
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2
public/2016-08/index.html
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@ -60,7 +60,7 @@ $ git rebase -i dspace-5.5
"/>
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2
public/2016-09/index.html
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@ -52,7 +52,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
"/>
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2
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@ -60,7 +60,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
"/>
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2
public/2016-11/index.html
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@ -44,7 +44,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
"/>
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2
public/2016-12/index.html
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@ -68,7 +68,7 @@ Another worrying error from dspace.log is:
"/>
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2
public/2017-01/index.html
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@ -44,7 +44,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
"/>
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2
public/2017-02/index.html
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@ -72,7 +72,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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2
public/2017-03/index.html
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@ -76,7 +76,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
"/>
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2
public/2017-04/index.html
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@ -62,7 +62,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
"/>
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<meta name="generator" content="Hugo 0.33" />

2
public/2017-05/index.html
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@ -28,7 +28,7 @@
<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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2
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@ -28,7 +28,7 @@
<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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2
public/2017-07/index.html
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@ -56,7 +56,7 @@ We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the
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2
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@ -76,7 +76,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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2
public/2017-09/index.html
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@ -52,7 +52,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
"/>
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2
public/2017-10/index.html
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@ -56,7 +56,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
"/>
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2
public/2017-11/index.html
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@ -76,7 +76,7 @@ COPY 54701
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2
public/2017-12/index.html
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@ -46,7 +46,7 @@ The list of connections to XMLUI and REST API for today:
"/>
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20
public/2018-01/index.html
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@ -92,7 +92,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
<meta property="article:modified_time" content="2018-01-17T18:53:01&#43;02:00"/>
<meta property="article:modified_time" content="2018-01-18T10:24:57&#43;02:00"/>
@ -184,7 +184,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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@ -194,9 +194,9 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
"@type": "BlogPosting",
"headline": "January, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-01/",
"wordCount": "4985",
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"datePublished": "2018-01-02T08:35:54-08:00",
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@ -1252,9 +1252,21 @@ Jan 18 07:01:22 linode18 sudo[10812]: pam_unix(sudo:session): session opened for
</code></pre>
<ul>
<li>I had to cancel the Discovery indexing and I&rsquo;ll have to re-try it another time when the server isn&rsquo;t so busy (it had already taken two hours and wasn&rsquo;t even close to being done)</li>
<li>For now I&rsquo;ve increased the Tomcat JVM heap from 5632 to 6144m, to give ~1GB of free memory over the average usage to hopefully account for spikes caused by load or background jobs</li>
</ul>
<h2 id="2018-01-19">2018-01-19</h2>
<ul>
<li>Linode alerted and said that the CPU load was 264% on CGSpace</li>
<li>Start the Discovery indexing again:</li>
</ul>
<pre><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx1024m -XX:+TieredCompilation -XX:TieredStopAtLevel=1&quot;
$ time schedtool -D -e ionice -c2 -n7 nice -n19 /home/cgspace.cgiar.org/bin/dspace index-discovery -b
</code></pre>

168
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@ -0,0 +1,168 @@
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<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="Categories" />
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Categories"/>
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"keywords": "notes,notes,",
"description": "Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/categories/">
<title>CGSpace Notes</title>
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<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"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description">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">
</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/2018-01/">January, 2018</a></li>
<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</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>
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>
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2
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@ -25,7 +25,7 @@
<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Notes"/>
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1
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@ -0,0 +1 @@
<!DOCTYPE html><html><head><title>https://alanorth.github.io/cgspace-notes/categories/</title><link rel="canonical" href="https://alanorth.github.io/cgspace-notes/categories/"/><meta name="robots" content="noindex"><meta http-equiv="content-type" content="text/html; charset=utf-8" /><meta http-equiv="refresh" content="0; url=https://alanorth.github.io/cgspace-notes/categories/" /></head></html>

2
public/cgiar-library-migration/index.html
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@ -28,7 +28,7 @@
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2
public/index.html
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@ -25,7 +25,7 @@
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2
public/page/2/index.html
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@ -25,7 +25,7 @@
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2
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@ -25,7 +25,7 @@
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2
public/post/index.html
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@ -25,7 +25,7 @@
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2
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@ -25,7 +25,7 @@
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2
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@ -25,7 +25,7 @@
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2
public/robots.txt
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@ -31,7 +31,7 @@ Disallow: /cgspace-notes/2015-12/
Disallow: /cgspace-notes/2015-11/
Disallow: /cgspace-notes/
Disallow: /cgspace-notes/categories/
Disallow: /cgspace-notes/tags/notes/
Disallow: /cgspace-notes/categories/notes/
Disallow: /cgspace-notes/tags/notes/
Disallow: /cgspace-notes/post/
Disallow: /cgspace-notes/tags/

20
public/sitemap.xml
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@ -4,7 +4,7 @@
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@ -144,7 +144,7 @@
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@ -153,27 +153,27 @@
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<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></li>
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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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