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Add notes for 2023-03-21

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Alan Orth
2023-03-21 16:35:41 +03:00
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@ -16,7 +16,7 @@ I finally got through with porting the input form from DSpace 6 to DSpace 7
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-03/" />
<meta property="article:published_time" content="2023-03-01T07:58:36+03:00" />
<meta property="article:modified_time" content="2023-03-18T17:42:40+03:00" />
<meta property="article:modified_time" content="2023-03-19T19:48:06+03:00" />
@ -28,7 +28,7 @@ Remove cg.subject.wle and cg.identifier.wletheme from CGSpace input form after c
iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
I finally got through with porting the input form from DSpace 6 to DSpace 7
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@ -38,9 +38,9 @@ I finally got through with porting the input form from DSpace 6 to DSpace 7
"@type": "BlogPosting",
"headline": "March, 2023",
"url": "https://alanorth.github.io/cgspace-notes/2023-03/",
"wordCount": "2810",
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"datePublished": "2023-03-01T07:58:36+03:00",
"dateModified": "2023-03-18T17:42:40+03:00",
"dateModified": "2023-03-19T19:48:06+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -556,6 +556,61 @@ pd.options.mode.nullable_dtypes = True
<ul>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-03-20">2023-03-20</h2>
<ul>
<li>Minor updates to a few of my DSpace Python scripts to fix the logging</li>
<li>Minor updates to some records for Mazingira reported by Sonja</li>
<li>Upgrade PostgreSQL on DSpace Test from version 12 to 14, the same way I did from 10 to 12 last year:
<ul>
<li>First, I installed the new version of PostgreSQL via the Ansible playbook scripts</li>
<li>Then I stopped Tomcat and all PostgreSQL clusters and used <code>pg_upgrade</code> to upgrade the old version:</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># systemctl stop tomcat7
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">12</span> main stop
</span></span><span style="display:flex;"><span># tar -cvzpf var-lib-postgresql-12.tar.gz /var/lib/postgresql/12
</span></span><span style="display:flex;"><span># tar -cvzpf etc-postgresql-12.tar.gz /etc/postgresql/12
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">14</span> main stop
</span></span><span style="display:flex;"><span># pg_dropcluster <span style="color:#ae81ff">14</span> main
</span></span><span style="display:flex;"><span># pg_upgradecluster <span style="color:#ae81ff">12</span> main
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">14</span> main start
</span></span></code></pre></div><ul>
<li>After that I <a href="https://adamj.eu/tech/2021/04/13/reindexing-all-tables-after-upgrading-to-postgresql-13/">re-indexed the database indexes using a query</a>:</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>$ su - postgres
</span></span><span style="display:flex;"><span>$ cat /tmp/generate-reindex.sql
</span></span><span style="display:flex;"><span>SELECT &#39;REINDEX TABLE CONCURRENTLY &#39; || quote_ident(relname) || &#39; /*&#39; || pg_size_pretty(pg_total_relation_size(C.oid)) || &#39;*/;&#39;
</span></span><span style="display:flex;"><span>FROM pg_class C
</span></span><span style="display:flex;"><span>LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
</span></span><span style="display:flex;"><span>WHERE nspname = &#39;public&#39;
</span></span><span style="display:flex;"><span> AND C.relkind = &#39;r&#39;
</span></span><span style="display:flex;"><span> AND nspname !~ &#39;^pg_toast&#39;
</span></span><span style="display:flex;"><span>ORDER BY pg_total_relation_size(C.oid) ASC;
</span></span><span style="display:flex;"><span>$ psql dspace &lt; /tmp/generate-reindex.sql &gt; /tmp/reindex.sql
</span></span><span style="display:flex;"><span>$ &lt;trim the extra stuff from /tmp/reindex.sql&gt;
</span></span><span style="display:flex;"><span>$ psql dspace &lt; /tmp/reindex.sql
</span></span></code></pre></div><ul>
<li>The index on <code>metadatavalue</code> shrunk by 90MB, and others a bit less
<ul>
<li>This is nice, but not as drastic as I noticed last year when upgrading to PostgreSQL 12</li>
</ul>
</li>
</ul>
<h2 id="2023-03-21">2023-03-21</h2>
<ul>
<li>Leigh sent me a list of IFPRI authors with ORCID identifiers so I combined them with our list and resolved all their names with <code>resolve_orcids.py</code>
<ul>
<li>It adds 154 new ORCID identifiers</li>
</ul>
</li>
<li>I did a follow up to the publisher names from last week using the list from doi.org
<ul>
<li>Last week I only updated items with a DOI that had <em>no</em> publisher, but now I was curious to see how our existing publisher information compared</li>
<li>I checked a dozen or so manually and, other than CIFOR/ICRAF and CIAT/Alliance, the metadata was better than our existing data, so I overwrote them</li>
</ul>
</li>
</ul>
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