mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-05 06:43:00 +01:00
530 lines
17 KiB
HTML
530 lines
17 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="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 property="og:updated_time" content="2017-09-18T16:38:35+03:00"/>
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="Categories"/>
|
|
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
|
<meta name="generator" content="Hugo 0.55.3" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "Blog",
|
|
"headline": "CGSpace Notes",
|
|
"url" : "https:\/\/alanorth.github.io\/cgspace-notes\/categories\/",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"dateModified": "2017-09-18T16:38:35\x2b03:00",
|
|
"keywords": "notes,notes,",
|
|
"description": "Documenting day-to-day work on the [CGSpace](https:\/\/cgspace.cgiar.org) repository."
|
|
}
|
|
</script>
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/categories/">
|
|
|
|
<title>CGSpace Notes</title>
|
|
|
|
<!-- combined, minified CSS -->
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-G5B34w7DFTumWTswxYzTX7NWfbvQEg1HbFFEg6ItN03uTAAoS2qkPS/fu3LhuuSA" crossorigin="anonymous">
|
|
|
|
<!-- RSS 2.0 feed -->
|
|
<link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/categories/index.xml" title="CGSpace Notes" />
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</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"><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">
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-07-01T12:56:54+03:00">Sun Jul 01, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-07-01">2018-07-01</h2>
|
|
|
|
<ul>
|
|
<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
|
|
</ul>
|
|
|
|
<pre><code>There is insufficient memory for the Java Runtime Environment to continue.
|
|
</code></pre>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-07/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-06/">June, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-06-04T19:49:54-07:00">Mon Jun 04, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-06-04">2018-06-04</h2>
|
|
|
|
<ul>
|
|
<li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>)
|
|
|
|
<ul>
|
|
<li>There seems to be a problem with the CUA and L&R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn’t build</li>
|
|
</ul></li>
|
|
<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
|
|
<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li>
|
|
<li>Time to index ~70,000 items on CGSpace:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
|
|
|
|
real 74m42.646s
|
|
user 8m5.056s
|
|
sys 2m7.289s
|
|
</code></pre>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-06/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-05/">May, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-05-01T16:43:54+03:00">Tue May 01, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-05-01">2018-05-01</h2>
|
|
|
|
<ul>
|
|
<li>I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
|
|
|
|
<ul>
|
|
<li><a href="http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E">http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E</a></li>
|
|
<li><a href="http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E">http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E</a></li>
|
|
</ul></li>
|
|
<li>Then I reduced the JVM heap size from 6144 back to 5120m</li>
|
|
<li>Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to support hosts choosing which distribution they want to use</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-05/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-04/">April, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-04-01T16:13:54+02:00">Sun Apr 01, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-04-01">2018-04-01</h2>
|
|
|
|
<ul>
|
|
<li>I tried to test something on DSpace Test but noticed that it’s down since god knows when</li>
|
|
<li>Catalina logs at least show some memory errors yesterday:</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-04/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-03/">March, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-03-02T16:07:54+02:00">Fri Mar 02, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-03-02">2018-03-02</h2>
|
|
|
|
<ul>
|
|
<li>Export a CSV of the IITA community metadata for Martin Mueller</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-03/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-02/">February, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-02-01T16:28:54+02:00">Thu Feb 01, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-02-01">2018-02-01</h2>
|
|
|
|
<ul>
|
|
<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
|
|
<li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li>
|
|
<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
|
|
<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu’s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-02/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2018-01-02">2018-01-02</h2>
|
|
|
|
<ul>
|
|
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
|
|
<li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li>
|
|
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
|
|
<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
|
|
<li>And just before that I see this:</li>
|
|
</ul>
|
|
|
|
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Ah hah! So the pool was actually empty!</li>
|
|
<li>I need to increase that, let’s try to bump it up from 50 to 75</li>
|
|
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</li>
|
|
<li>I notice this error quite a few times in dspace.log:</li>
|
|
</ul>
|
|
|
|
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
|
|
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>And there are many of these errors every day for the past month:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
|
|
dspace.log.2017-11-21:4
|
|
dspace.log.2017-11-22:1
|
|
dspace.log.2017-11-23:4
|
|
dspace.log.2017-11-24:11
|
|
dspace.log.2017-11-25:0
|
|
dspace.log.2017-11-26:1
|
|
dspace.log.2017-11-27:7
|
|
dspace.log.2017-11-28:21
|
|
dspace.log.2017-11-29:31
|
|
dspace.log.2017-11-30:15
|
|
dspace.log.2017-12-01:15
|
|
dspace.log.2017-12-02:20
|
|
dspace.log.2017-12-03:38
|
|
dspace.log.2017-12-04:65
|
|
dspace.log.2017-12-05:43
|
|
dspace.log.2017-12-06:72
|
|
dspace.log.2017-12-07:27
|
|
dspace.log.2017-12-08:15
|
|
dspace.log.2017-12-09:29
|
|
dspace.log.2017-12-10:35
|
|
dspace.log.2017-12-11:20
|
|
dspace.log.2017-12-12:44
|
|
dspace.log.2017-12-13:36
|
|
dspace.log.2017-12-14:59
|
|
dspace.log.2017-12-15:104
|
|
dspace.log.2017-12-16:53
|
|
dspace.log.2017-12-17:66
|
|
dspace.log.2017-12-18:83
|
|
dspace.log.2017-12-19:101
|
|
dspace.log.2017-12-20:74
|
|
dspace.log.2017-12-21:55
|
|
dspace.log.2017-12-22:66
|
|
dspace.log.2017-12-23:50
|
|
dspace.log.2017-12-24:85
|
|
dspace.log.2017-12-25:62
|
|
dspace.log.2017-12-26:49
|
|
dspace.log.2017-12-27:30
|
|
dspace.log.2017-12-28:54
|
|
dspace.log.2017-12-29:68
|
|
dspace.log.2017-12-30:89
|
|
dspace.log.2017-12-31:53
|
|
dspace.log.2018-01-01:45
|
|
dspace.log.2018-01-02:34
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-12/">December, 2017</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-12-01T13:53:54+03:00">Fri Dec 01, 2017</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2017-12-01">2017-12-01</h2>
|
|
|
|
<ul>
|
|
<li>Uptime Robot noticed that CGSpace went down</li>
|
|
<li>The logs say “Timeout waiting for idle object”</li>
|
|
<li>PostgreSQL activity says there are 115 connections currently</li>
|
|
<li>The list of connections to XMLUI and REST API for today:</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-12/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2017-11-01">2017-11-01</h2>
|
|
|
|
<ul>
|
|
<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
|
|
</ul>
|
|
|
|
<h2 id="2017-11-02">2017-11-02</h2>
|
|
|
|
<ul>
|
|
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
|
|
</ul>
|
|
|
|
<pre><code># grep -c "CORE" /var/log/nginx/access.log
|
|
0
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
|
|
</ul>
|
|
|
|
<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
|
|
COPY 54701
|
|
</code></pre>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2017-10-01">2017-10-01</h2>
|
|
|
|
<ul>
|
|
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
|
|
</ul>
|
|
|
|
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
|
|
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
|
|
</ul>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
<nav class="blog-pagination">
|
|
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/" rel="prev" role="button">Previous page</a>
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/page/3/" rel="next" role="button">Next page</a>
|
|
|
|
|
|
|
|
</nav>
|
|
|
|
|
|
|
|
|
|
|
|
</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/2019-05/">May, 2019</a></li>
|
|
|
|
<li><a href="/cgspace-notes/posts/">Posts</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2019-02/">February, 2019</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>
|
|
</p>
|
|
</footer>
|
|
|
|
|
|
</body>
|
|
|
|
</html>
|