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277 lines
9.8 KiB
HTML
277 lines
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="June, 2020" />
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<meta property="og:description" content="2020-06-01
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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
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I sent Atmire the dspace.log from today and told them to log into the server to debug the process
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In other news, I checked the statistics API on DSpace 6 and it’s working
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I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-06/" />
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<meta property="article:published_time" content="2020-06-01T13:55:39+03:00" />
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<meta property="article:modified_time" content="2020-06-01T17:08:25+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="June, 2020"/>
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<meta name="twitter:description" content="2020-06-01
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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
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I sent Atmire the dspace.log from today and told them to log into the server to debug the process
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In other news, I checked the statistics API on DSpace 6 and it’s working
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I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
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<meta name="generator" content="Hugo 0.71.1" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "June, 2020",
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"url": "https://alanorth.github.io/cgspace-notes/2020-06/",
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"wordCount": "386",
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"datePublished": "2020-06-01T13:55:39+03:00",
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"dateModified": "2020-06-01T17:08:25+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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"keywords": "Notes"
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}
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</script>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-06/">
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<title>June, 2020 | CGSpace Notes</title>
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<link href="https://alanorth.github.io/cgspace-notes/css/style.6da5c906cc7a8fbb93f31cd2316c5dbe3f19ac4aa6bfb066f1243045b8f6061e.css" rel="stylesheet" integrity="sha256-baXJBsx6j7uT8xzSMWxdvj8ZrEqmv7Bm8SQwRbj2Bh4=" crossorigin="anonymous">
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<!-- minified Font Awesome for SVG icons -->
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<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f3d2a1f5980bab30ddd0d8cadbd496475309fc48e2b1d052c5c09e6facffcb0f.js" integrity="sha256-89Kh9ZgLqzDd0NjK29SWR1MJ/EjisdBSxcCeb6z/yw8=" crossorigin="anonymous"></script>
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2020-06-01">2020-06-01</h2>
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<ul>
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<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
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<ul>
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<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
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</ul>
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</li>
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<li>In other news, I checked the statistics API on DSpace 6 and it’s working</li>
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<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
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</ul>
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<pre><code>$ dspace oai import -c
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OAI 2.0 manager action started
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Loading @mire database changes for module MQM
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Changes have been processed
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Clearing index
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Index cleared
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Using full import.
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Full import
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java.lang.NullPointerException
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at org.dspace.xoai.app.XOAI.willChangeStatus(XOAI.java:438)
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at org.dspace.xoai.app.XOAI.index(XOAI.java:368)
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at org.dspace.xoai.app.XOAI.index(XOAI.java:280)
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at org.dspace.xoai.app.XOAI.indexAll(XOAI.java:227)
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at org.dspace.xoai.app.XOAI.index(XOAI.java:134)
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at org.dspace.xoai.app.XOAI.main(XOAI.java:560)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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</code></pre><h2 id="2020-06-02">2020-06-02</h2>
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<ul>
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<li>I noticed that I was able to do a partial OAI import (ie, without <code>-c</code>)
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<ul>
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<li>Then I tried to clear the OAI Solr core and import, but I get the same error:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ curl http://localhost:8080/solr/oai/update -H "Content-type: text/xml" --data-binary '<delete><query>*:*</query></delete>'
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$ curl http://localhost:8080/solr/oai/update -H "Content-type: text/xml" --data-binary '<commit />'
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$ ~/dspace63/bin/dspace oai import
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OAI 2.0 manager action started
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...
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There are no indexed documents, using full import.
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Full import
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java.lang.NullPointerException
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at org.dspace.xoai.app.XOAI.willChangeStatus(XOAI.java:438)
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at org.dspace.xoai.app.XOAI.index(XOAI.java:368)
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at org.dspace.xoai.app.XOAI.index(XOAI.java:280)
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at org.dspace.xoai.app.XOAI.indexAll(XOAI.java:227)
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at org.dspace.xoai.app.XOAI.index(XOAI.java:143)
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at org.dspace.xoai.app.XOAI.main(XOAI.java:560)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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</code></pre><ul>
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<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
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<ul>
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<li>They suspect it has to do with the item having some missing group names in its authorization policies</li>
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<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>
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<li>Indeed there are some blank group names:</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2020/06/item-authorizations-dspace63.png" alt="Missing group names in DSpace 6.3 item authorization policy"></p>
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<ul>
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<li>The same item on CGSpace (DSpace 5.8) also has groups with no name:</li>
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</ul>
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<p><img src="/cgspace-notes/2020/06/item-authorizations-dspace58.png" alt="Missing group names in DSpace 5.8 item authorization policy"></p>
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<ul>
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<li>I added some debugging and found exactly where this happens
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<ul>
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<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>
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<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>
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<li>I cherry picked 150e83558103ed7f50e8f323b6407b9cbdf33717 into our current <code>6_x-dev-atmire-modules</code> branch</li>
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</ul>
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</li>
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</ul>
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<!-- raw HTML omitted -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2020-06/">June, 2020</a></li>
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<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
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<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
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<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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</p>
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<p>
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<a href="#">Back to top</a>
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</p>
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</footer>
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</body>
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</html>
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