mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-05 06:43:00 +01:00
277 lines
9.8 KiB
HTML
277 lines
9.8 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="June, 2020" />
|
||
|
|
<meta property="og:description" content="2020-06-01
|
||
|
|
|
||
|
|
I tried to run the AtomicStatisticsUpdateCLI CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
|
||
|
|
|
||
|
|
I sent Atmire the dspace.log from today and told them to log into the server to debug the process
|
||
|
|
|
||
|
|
|
||
|
|
In other news, I checked the statistics API on DSpace 6 and it’s working
|
||
|
|
I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
|
||
|
|
" />
|
||
|
|
<meta property="og:type" content="article" />
|
||
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-06/" />
|
||
|
|
<meta property="article:published_time" content="2020-06-01T13:55:39+03:00" />
|
||
|
|
<meta property="article:modified_time" content="2020-06-01T17:08:25+03:00" />
|
||
|
|
|
||
|
|
<meta name="twitter:card" content="summary"/>
|
||
|
|
<meta name="twitter:title" content="June, 2020"/>
|
||
|
|
<meta name="twitter:description" content="2020-06-01
|
||
|
|
|
||
|
|
I tried to run the AtomicStatisticsUpdateCLI CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
|
||
|
|
|
||
|
|
I sent Atmire the dspace.log from today and told them to log into the server to debug the process
|
||
|
|
|
||
|
|
|
||
|
|
In other news, I checked the statistics API on DSpace 6 and it’s working
|
||
|
|
I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
|
||
|
|
"/>
|
||
|
|
<meta name="generator" content="Hugo 0.71.1" />
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
<script type="application/ld+json">
|
||
|
|
{
|
||
|
|
"@context": "http://schema.org",
|
||
|
|
"@type": "BlogPosting",
|
||
|
|
"headline": "June, 2020",
|
||
|
|
"url": "https://alanorth.github.io/cgspace-notes/2020-06/",
|
||
|
|
"wordCount": "386",
|
||
|
|
"datePublished": "2020-06-01T13:55:39+03:00",
|
||
|
|
"dateModified": "2020-06-01T17:08:25+03:00",
|
||
|
|
"author": {
|
||
|
|
"@type": "Person",
|
||
|
|
"name": "Alan Orth"
|
||
|
|
},
|
||
|
|
"keywords": "Notes"
|
||
|
|
}
|
||
|
|
</script>
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-06/">
|
||
|
|
|
||
|
|
<title>June, 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/2020-06/">June, 2020</a></h2>
|
||
|
|
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 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="2020-06-01">2020-06-01</h2>
|
||
|
|
<ul>
|
||
|
|
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
|
||
|
|
<ul>
|
||
|
|
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
|
||
|
|
</ul>
|
||
|
|
</li>
|
||
|
|
<li>In other news, I checked the statistics API on DSpace 6 and it’s working</li>
|
||
|
|
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
|
||
|
|
</ul>
|
||
|
|
<pre><code>$ dspace oai import -c
|
||
|
|
OAI 2.0 manager action started
|
||
|
|
Loading @mire database changes for module MQM
|
||
|
|
Changes have been processed
|
||
|
|
Clearing index
|
||
|
|
Index cleared
|
||
|
|
Using full import.
|
||
|
|
Full import
|
||
|
|
java.lang.NullPointerException
|
||
|
|
at org.dspace.xoai.app.XOAI.willChangeStatus(XOAI.java:438)
|
||
|
|
at org.dspace.xoai.app.XOAI.index(XOAI.java:368)
|
||
|
|
at org.dspace.xoai.app.XOAI.index(XOAI.java:280)
|
||
|
|
at org.dspace.xoai.app.XOAI.indexAll(XOAI.java:227)
|
||
|
|
at org.dspace.xoai.app.XOAI.index(XOAI.java:134)
|
||
|
|
at org.dspace.xoai.app.XOAI.main(XOAI.java:560)
|
||
|
|
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||
|
|
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
||
|
|
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||
|
|
at java.lang.reflect.Method.invoke(Method.java:498)
|
||
|
|
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
|
||
|
|
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
|
||
|
|
</code></pre><h2 id="2020-06-02">2020-06-02</h2>
|
||
|
|
<ul>
|
||
|
|
<li>I noticed that I was able to do a partial OAI import (ie, without <code>-c</code>)
|
||
|
|
<ul>
|
||
|
|
<li>Then I tried to clear the OAI Solr core and import, but I get the same error:</li>
|
||
|
|
</ul>
|
||
|
|
</li>
|
||
|
|
</ul>
|
||
|
|
<pre><code>$ curl http://localhost:8080/solr/oai/update -H "Content-type: text/xml" --data-binary '<delete><query>*:*</query></delete>'
|
||
|
|
$ curl http://localhost:8080/solr/oai/update -H "Content-type: text/xml" --data-binary '<commit />'
|
||
|
|
$ ~/dspace63/bin/dspace oai import
|
||
|
|
OAI 2.0 manager action started
|
||
|
|
...
|
||
|
|
There are no indexed documents, using full import.
|
||
|
|
Full import
|
||
|
|
java.lang.NullPointerException
|
||
|
|
at org.dspace.xoai.app.XOAI.willChangeStatus(XOAI.java:438)
|
||
|
|
at org.dspace.xoai.app.XOAI.index(XOAI.java:368)
|
||
|
|
at org.dspace.xoai.app.XOAI.index(XOAI.java:280)
|
||
|
|
at org.dspace.xoai.app.XOAI.indexAll(XOAI.java:227)
|
||
|
|
at org.dspace.xoai.app.XOAI.index(XOAI.java:143)
|
||
|
|
at org.dspace.xoai.app.XOAI.main(XOAI.java:560)
|
||
|
|
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||
|
|
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
||
|
|
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||
|
|
at java.lang.reflect.Method.invoke(Method.java:498)
|
||
|
|
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
|
||
|
|
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
|
||
|
|
</code></pre><ul>
|
||
|
|
<li>I found a <a href="https://jira.lyrasis.org/browse/DS-4363">bug report on DSpace Jira</a> describing this issue affecting someone else running DSpace 6.3
|
||
|
|
<ul>
|
||
|
|
<li>They suspect it has to do with the item having some missing group names in its authorization policies</li>
|
||
|
|
<li>I added some debugging to <code>dspace-oai/src/main/java/org/dspace/xoai/app/XOAI.java</code> to print the Handle of the item that causes the crash and then I looked at its authorization policies</li>
|
||
|
|
<li>Indeed there are some blank group names:</li>
|
||
|
|
</ul>
|
||
|
|
</li>
|
||
|
|
</ul>
|
||
|
|
<p><img src="/cgspace-notes/2020/06/item-authorizations-dspace63.png" alt="Missing group names in DSpace 6.3 item authorization policy"></p>
|
||
|
|
<ul>
|
||
|
|
<li>The same item on CGSpace (DSpace 5.8) also has groups with no name:</li>
|
||
|
|
</ul>
|
||
|
|
<p><img src="/cgspace-notes/2020/06/item-authorizations-dspace58.png" alt="Missing group names in DSpace 5.8 item authorization policy"></p>
|
||
|
|
<ul>
|
||
|
|
<li>I added some debugging and found exactly where this happens
|
||
|
|
<ul>
|
||
|
|
<li>As it turns out we can just check if the group policy is null there and it allows the OAI import to proceed</li>
|
||
|
|
<li>Aaaaand as it turns out, this was fixed in <code>dspace-6_x</code> in 2018 after DSpace 6.3 was released (see <a href="https://jira.lyrasis.org/browse/DS-4019">DS-4019</a>), so that was a waste of three hours.</li>
|
||
|
|
<li>I cherry picked 150e83558103ed7f50e8f323b6407b9cbdf33717 into our current <code>6_x-dev-atmire-modules</code> branch</li>
|
||
|
|
</ul>
|
||
|
|
</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/2020-06/">June, 2020</a></li>
|
||
|
|
|
||
|
|
<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
|
||
|
|
|
||
|
|
<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
|
||
|
|
|
||
|
|
<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
|
||
|
|
|
||
|
|
<li><a href="/cgspace-notes/2020-02/">February, 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>
|