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I finally got around to working on Peter’s cleanups for affiliations, authors, and donors from last week
I did some minor cleanups myself and applied them to CGSpace
Start working on some batch uploads for IFPRI
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I finally got around to working on Peter’s cleanups for affiliations, authors, and donors from last week
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<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>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-08/">August, 2023</a></h2>
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<time datetime="2023-08-03T11:18:36+03:00">Thu Aug 03, 2023</time>
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<h2 id="2023-08-03">2023-08-03</h2>
<ul>
<li>I finally got around to working on Peter’s cleanups for affiliations, authors, and donors from last week
<ul>
<li>I did some minor cleanups myself and applied them to CGSpace</li>
</ul>
</li>
<li>Start working on some batch uploads for IFPRI</li>
</ul>
<h2 id="2023-08-04">2023-08-04</h2>
<ul>
<li>Minor cleanups on IFPRI’s batch uploads
<ul>
<li>I also did a duplicate check and found thirteen items that seem to be duplicates, so I sent them to Leigh to check</li>
</ul>
</li>
<li>I read this <a href="https://www.endpointdev.com/blog/2012/06/logstatement-postgres-all-full-logging/">interesting blog post about PostgreSQL’s <code>log_statement</code> function</a>
<ul>
<li>Someone pointed out that this also lets you take advantage of <a href="https://github.com/darold/pgbadger">PgBadger</a> analysis</li>
<li>I enabled statement logging on DSpace Test and I will check it in a few days</li>
</ul>
</li>
<li>Reading about DSpace 7 REST API again
<ul>
<li>Here is how to get the first page of 100 items: <a href="https://dspace7test.ilri.org/server/api/discover/search/objects?dsoType=item&page=1&size=100">https://dspace7test.ilri.org/server/api/discover/search/objects?dsoType=item&page=1&size=100</a></li>
<li>I really want to benchmark this to see how fast we can get all the pages</li>
<li>Another thing I notice is that the bitstreams are not here, so that will be an extra call…</li>
</ul>
</li>
</ul>
<h2 id="2023-08-05">2023-08-05</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-08-07">2023-08-07</h2>
<ul>
<li>I’m checking the PostgreSQL logs now that statement logging has been enabled for a few days on DSpace Test
<ul>
<li>I see the logs are about 7 or 8 GB, which is larger than expected—and this is the test server!</li>
<li>I will now play with pgbadger to see if it gives any useful insights</li>
<li>Hmm, it sems the <code>log_statement</code> advice was old as pgbadger itself says:</li>
</ul>
</li>
</ul>
<blockquote>
<p>Do not enable log_statement as its log format will not be parsed by pgBadger.</p>
</blockquote>
<p>… and:</p>
<blockquote>
<p>Warning: Do not enable both log_min_duration_statement, log_duration and log_statement all together, this will result in wrong counter values. Note that this will also increase drastically the size of your log. log_min_duration_statement should always be preferred.</p>
</blockquote>
<ul>
<li>So we need to follow pgbadger’s instructions rather to get a suitable log file
<ul>
<li>After enabling the new settings I see that our log file is going to be reaallllly big… hmmmm will check tomorrow morning</li>
</ul>
</li>
<li>More work on the IFPRI batch uploads</li>
</ul>
<h2 id="2023-08-08">2023-08-08</h2>
<ul>
<li>Apply more corrections to authors from Peter on CGSpace</li>
<li>I finally figured out a <code>log_line_prefix</code> for PostgreSQL that works for pgBadger:</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>log_line_prefix = '%t [%p]: user=%u,db=%d,app=%a,client=%h '
</span></span></code></pre></div><ul>
<li>Now I can generate reports:</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># /usr/bin/pgbadger -I -q /var/log/postgresql/postgresql-14-main.log -O /srv/www/pgbadger
</span></span></code></pre></div><ul>
<li>Ideally we would run this incremental report every day on the postgresql-14-main.log.1 aka yesterday’s version of the log file after it is rotated
<ul>
<li>Now I have to see how large the file will be…</li>
</ul>
</li>
<li>I did some final updates to the ninety IFPRI records and uploaded them to DSpace Test first, then to CGSpace</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2023-08/">August, 2023</a></li>
<li><a href="/cgspace-notes/2023-07/">July, 2023</a></li>
<li><a href="/cgspace-notes/2023-06/">June, 2023</a></li>
<li><a href="/cgspace-notes/2023-05/">May, 2023</a></li>
<li><a href="/cgspace-notes/2023-04/">April, 2023</a></li>
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<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>
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