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238 lines
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HTML
238 lines
8.5 KiB
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<meta property="og:title" content="January, 2023" />
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<meta property="og:description" content="2023-01-01
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Apply some more ORCID identifiers to items on CGSpace using my 2022-09-22-add-orcids.csv file
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I want to update all ORCID names and refresh them in the database
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I see we have some new ones that aren’t in our list if I combine with this file:
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" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-01/" />
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<meta property="article:published_time" content="2023-01-01T08:44:36+03:00" />
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<meta property="article:modified_time" content="2023-01-01T08:44:36+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="January, 2023"/>
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<meta name="twitter:description" content="2023-01-01
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Apply some more ORCID identifiers to items on CGSpace using my 2022-09-22-add-orcids.csv file
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I want to update all ORCID names and refresh them in the database
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I see we have some new ones that aren’t in our list if I combine with this file:
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"/>
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"@type": "BlogPosting",
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"headline": "January, 2023",
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"url": "https://alanorth.github.io/cgspace-notes/2023-01/",
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"datePublished": "2023-01-01T08:44:36+03:00",
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"dateModified": "2023-01-01T08:44:36+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2023-01/">
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<title>January, 2023 | CGSpace Notes</title>
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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/2023-01/">January, 2023</a></h2>
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<p class="blog-post-meta">
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<time datetime="2023-01-01T08:44:36+03:00">Sun Jan 01, 2023</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2023-01-01">2023-01-01</h2>
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<ul>
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<li>Apply some more ORCID identifiers to items on CGSpace using my <code>2022-09-22-add-orcids.csv</code> file
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<ul>
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<li>I want to update all ORCID names and refresh them in the database</li>
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<li>I see we have some new ones that aren’t in our list if I combine with this file:</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep - oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u | wc -l
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</span></span><span style="display:flex;"><span>1939
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</span></span><span style="display:flex;"><span>$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml 2022-09-22-add-orcids.csv| grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u | wc -l
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</span></span><span style="display:flex;"><span>1973
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</span></span></code></pre></div><ul>
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<li>I will extract and process them with my <code>resolve-orcids.py</code> script:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml 2022-09-22-add-orcids.csv| grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u > /tmp/2023-01-01-orcids.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/resolve-orcids.py -i /tmp/2023-01-01-orcids.txt -o /tmp/2023-01-01-orcids-names.txt -d
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</span></span></code></pre></div><ul>
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<li></li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/update-orcids.py -i /tmp/2023-01-01-orcids-names.txt -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -m <span style="color:#ae81ff">247</span>
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</span></span></code></pre></div><ul>
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<li>Load on CGSpace is high around 9.x
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<ul>
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<li>I see there is a CIAT bot harvesting via the REST API with IP 45.5.186.2</li>
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<li>Other than that I don’t see any particular system stats as alarming</li>
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<li>There has been a marked increase in load in the last few weeks, perhaps due to Initiative activity…</li>
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<li>Perhaps there are some stuck PostgreSQL locks from CLI tools?</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql -c <span style="color:#e6db74">'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;'</span> | grep -o -E <span style="color:#e6db74">'(dspaceWeb|dspaceApi|dspaceCli)'</span> | sort | uniq -c
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</span></span><span style="display:flex;"><span> 58 dspaceCli
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</span></span><span style="display:flex;"><span> 46 dspaceWeb
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</span></span></code></pre></div><ul>
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<li>The current time on the server is 08:52 and I see the dspaceCli locks were started at 04:00 and 05:00… so I need to check which cron jobs those belong to as I think I noticed this last month too
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<ul>
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<li>I’m going to wait and see if they finish, but by tomorrow I will kill them</li>
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</ul>
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</li>
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</ul>
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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/2023-01/">January, 2023</a></li>
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<li><a href="/cgspace-notes/2022-12/">December, 2022</a></li>
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<li><a href="/cgspace-notes/2022-11/">November, 2022</a></li>
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<li><a href="/cgspace-notes/2022-10/">October, 2022</a></li>
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<li><a href="/cgspace-notes/2022-09/">September, 2022</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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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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<a href="#">Back to top</a>
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