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Apply some more ORCID identifiers to items on CGSpace using my 2022-09-22-add-orcids.csv file
I want to update all ORCID names and refresh them in the database
I see we have some new ones that aren&rsquo;t in our list if I combine with this file:
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Apply some more ORCID identifiers to items on CGSpace using my 2022-09-22-add-orcids.csv file
I want to update all ORCID names and refresh them in the database
I see we have some new ones that aren&rsquo;t in our list if I combine with this file:
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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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<time datetime="2023-01-01T08:44:36+03:00">Sun Jan 01, 2023</time>
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<h2 id="2023-01-01">2023-01-01</h2>
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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
<ul>
<li>I want to update all ORCID names and refresh them in the database</li>
<li>I see we have some new ones that aren&rsquo;t in our list if I combine with this file:</li>
</ul>
</li>
</ul>
<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">&#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39;</span> | sort -u | wc -l
</span></span><span style="display:flex;"><span>1939
</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">&#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39;</span> | sort -u | wc -l
</span></span><span style="display:flex;"><span>1973
</span></span></code></pre></div><ul>
<li>I will extract and process them with my <code>resolve-orcids.py</code> script:</li>
</ul>
<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">&#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39;</span> | sort -u &gt; /tmp/2023-01-01-orcids.txt
</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
</span></span></code></pre></div><ul>
<li></li>
</ul>
<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">&#39;fuuu&#39;</span> -m <span style="color:#ae81ff">247</span>
</span></span></code></pre></div><ul>
<li>Load on CGSpace is high around 9.x
<ul>
<li>I see there is a CIAT bot harvesting via the REST API with IP 45.5.186.2</li>
<li>Other than that I don&rsquo;t see any particular system stats as alarming</li>
<li>There has been a marked increase in load in the last few weeks, perhaps due to Initiative activity&hellip;</li>
<li>Perhaps there are some stuck PostgreSQL locks from CLI tools?</li>
</ul>
</li>
</ul>
<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">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | grep -o -E <span style="color:#e6db74">&#39;(dspaceWeb|dspaceApi|dspaceCli)&#39;</span> | sort | uniq -c
</span></span><span style="display:flex;"><span> 58 dspaceCli
</span></span><span style="display:flex;"><span> 46 dspaceWeb
</span></span></code></pre></div><ul>
<li>The current time on the server is 08:52 and I see the dspaceCli locks were started at 04:00 and 05:00&hellip; so I need to check which cron jobs those belong to as I think I noticed this last month too
<ul>
<li>I&rsquo;m going to wait and see if they finish, but by tomorrow I will kill them</li>
</ul>
</li>
</ul>
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<li><a href="/cgspace-notes/2023-01/">January, 2023</a></li>
<li><a href="/cgspace-notes/2022-12/">December, 2022</a></li>
<li><a href="/cgspace-notes/2022-11/">November, 2022</a></li>
<li><a href="/cgspace-notes/2022-10/">October, 2022</a></li>
<li><a href="/cgspace-notes/2022-09/">September, 2022</a></li>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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