mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-23 13:34:32 +01:00
257 lines
8.7 KiB
HTML
257 lines
8.7 KiB
HTML
<!DOCTYPE html>
|
|
<html lang="en">
|
|
|
|
<head>
|
|
|
|
|
|
|
|
|
|
<meta charset="utf-8">
|
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
|
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
|
|
|
|
<meta name="description" content="">
|
|
<meta name="author" content="Alan Orth">
|
|
|
|
<!-- OpenGraph Metadata: http://ogp.me/ -->
|
|
<meta property="og:title" content="November, 2016">
|
|
<meta property="og:description" content="">
|
|
|
|
|
|
<meta property="og:type" content="article">
|
|
<meta property="article:published_time" content="2016-11-01T09:21:00+03:00">
|
|
<meta property="article:author" content="Alan Orth">
|
|
|
|
|
|
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-11/">
|
|
|
|
<!-- Metadata for Twitter: https://dev.twitter.com/cards/markup -->
|
|
|
|
<meta property="twitter:card" content="summary">
|
|
|
|
|
|
<meta property="twitter:title" content="November, 2016">
|
|
<meta property="twitter:description" content="">
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<meta name="generator" content="Hugo 0.17" />
|
|
|
|
|
|
<base href="https://alanorth.github.io/cgspace-notes/">
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2016-11/">
|
|
|
|
<title>November, 2016 | CGSpace Notes</title>
|
|
|
|
<!-- combined, minified CSS -->
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet">
|
|
|
|
<!-- RSS 2.0 feed -->
|
|
<link href="https://alanorth.github.io/cgspace-notes/index.xml" type="application/rss+xml" rel="alternate">
|
|
</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>
|
|
|
|
</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/2016-11/">November, 2016</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2016-11-01T09:21:00+03:00">Tue Nov 01, 2016</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="2016-11-01">2016-11-01</h2>
|
|
|
|
<ul>
|
|
<li>Add <code>dc.type</code> to the output options for Atmire’s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
|
|
</ul>
|
|
|
|
<p><img src="2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
|
|
|
|
<h2 id="2016-11-02">2016-11-02</h2>
|
|
|
|
<ul>
|
|
<li>Migrate DSpace Test to DSpace 5.5 (<a href="https://gist.github.com/alanorth/61013895c6efe7095d7f81000953d1cf">notes</a>)</li>
|
|
<li>Run all updates on DSpace Test and reboot the server</li>
|
|
<li>Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (<a href="https://github.com/ilri/DSpace/issues/63">#63</a>)</li>
|
|
<li>Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes</li>
|
|
<li>At the end it appeared to finish correctly but there were lots of errors right after it finished:</li>
|
|
</ul>
|
|
|
|
<pre><code>2016-11-02 15:09:48,578 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76454 to Index
|
|
2016-11-02 15:09:48,584 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Community: 10568/3202 to Index
|
|
2016-11-02 15:09:48,589 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76455 to Index
|
|
2016-11-02 15:09:48,590 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Community: 10568/51693 to Index
|
|
2016-11-02 15:09:48,590 INFO org.dspace.discovery.IndexClient @ Done with indexing
|
|
2016-11-02 15:09:48,600 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76456 to Index
|
|
2016-11-02 15:09:48,613 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/55536 to Index
|
|
2016-11-02 15:09:48,616 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76457 to Index
|
|
2016-11-02 15:09:48,634 ERROR com.atmire.dspace.discovery.AtmireSolrService @
|
|
java.lang.NullPointerException
|
|
at org.dspace.discovery.SearchUtils.getDiscoveryConfiguration(SourceFile:57)
|
|
at org.dspace.discovery.SolrServiceImpl.buildDocument(SolrServiceImpl.java:824)
|
|
at com.atmire.dspace.discovery.AtmireSolrService.indexContent(AtmireSolrService.java:821)
|
|
at com.atmire.dspace.discovery.AtmireSolrService.updateIndex(AtmireSolrService.java:898)
|
|
at org.dspace.discovery.SolrServiceImpl.createIndex(SolrServiceImpl.java:370)
|
|
at org.dspace.storage.rdbms.DatabaseUtils$ReindexerThread.run(DatabaseUtils.java:945)
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>DSpace is still up, and a few minutes later I see the default DSpace indexer is still running</li>
|
|
<li>Sure enough, looking back before the first one finished, I see output from both indexers interleaved in the log:</li>
|
|
</ul>
|
|
|
|
<pre><code>2016-11-02 15:09:28,545 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/47242 to Index
|
|
2016-11-02 15:09:28,633 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/60785 to Index
|
|
2016-11-02 15:09:28,678 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (55695 of 55722): 43557
|
|
2016-11-02 15:09:28,688 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (55703 of 55722): 34476
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I will raise a ticket with Atmire to ask them</li>
|
|
</ul>
|
|
|
|
<h2 id="2016-11-06">2016-11-06</h2>
|
|
|
|
<ul>
|
|
<li>After re-deploying and re-indexing I didn’t see the same issue, and the indexing completed in 85 minutes, which is about how long it is supposed to take</li>
|
|
</ul>
|
|
|
|
<h2 id="2016-11-07">2016-11-07</h2>
|
|
|
|
<ul>
|
|
<li>Horrible one liner to get Linode ID from certain Ansible host vars:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -A 3 contact_info * | grep -E "(Orth|Sisay|Peter|Daniel|Tsega)" | awk -F'-' '{print $1}' | grep linode | uniq | xargs grep linode_id
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I noticed some weird CRPs in the database, and they don’t show up in Discovery for some reason, perhaps the <code>:</code></li>
|
|
<li>I’ll export these and fix them in batch:</li>
|
|
</ul>
|
|
|
|
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=230 group by text_value order by count desc) to /tmp/crp.csv with csv;
|
|
COPY 22
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Test running the replacements:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ ./fix-metadata-values.py -i /tmp/CRPs.csv -f cg.contributor.crp -t correct -m 230 -d dspace -u dspace -p 'fuuu'
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Add <code>AMR</code> to ILRI subjects and remove one duplicate instance of IITA in author affiliations controlled vocabulary (<a href="https://github.com/ilri/DSpace/pull/288">#288</a>)</li>
|
|
</ul>
|
|
|
|
<h2 id="2016-11-08">2016-11-08</h2>
|
|
|
|
<ul>
|
|
<li>Atmire’s Listings and Reports module seems to be broken on DSpace 5.5</li>
|
|
</ul>
|
|
|
|
<p><img src="2016/11/listings-and-reports-55.png" alt="Listings and Reports broken in DSpace 5.5" /></p>
|
|
|
|
<ul>
|
|
<li>I’ve filed a ticket with Atmire</li>
|
|
</ul>
|
|
|
|
|
|
|
|
|
|
</article>
|
|
|
|
|
|
</div> <!-- /.blog-main -->
|
|
|
|
|
|
<aside class="col-sm-3 offset-sm-1 blog-sidebar">
|
|
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
<li><a href="/cgspace-notes/2016-11/">November, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2016-07/">July, 2016</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>
|