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271 lines
9.2 KiB
HTML
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<meta property="og:title" content="December, 2021" />
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<meta property="og:description" content="2021-12-01
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Atmire merged some changes I had submitted to the COUNTER-Robots project
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I updated our local spider user agents and then re-ran the list with my check-spider-hits.sh script on CGSpace:
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$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
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Purging 1989 hits from The Knowledge AI in statistics
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Purging 1235 hits from MaCoCu in statistics
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Purging 455 hits from WhatsApp in statistics
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Total number of bot hits purged: 3679
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" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="December, 2021"/>
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<meta name="twitter:description" content="2021-12-01
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Atmire merged some changes I had submitted to the COUNTER-Robots project
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I updated our local spider user agents and then re-ran the list with my check-spider-hits.sh script on CGSpace:
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$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
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Purging 1989 hits from The Knowledge AI in statistics
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Purging 1235 hits from MaCoCu in statistics
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Purging 455 hits from WhatsApp in statistics
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Total number of bot hits purged: 3679
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"/>
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"@type": "BlogPosting",
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"headline": "December, 2021",
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"url": "https://alanorth.github.io/cgspace-notes/2021-12/",
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<title>December, 2021 | CGSpace Notes</title>
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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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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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-12/">December, 2021</a></h2>
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<p class="blog-post-meta">
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<time datetime="2021-12-01T16:07:07+02:00">Wed Dec 01, 2021</time>
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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="2021-12-01">2021-12-01</h2>
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<ul>
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<li>Atmire merged some changes I had submitted to the COUNTER-Robots project</li>
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<li>I updated our local spider user agents and then re-ran the list with my <code>check-spider-hits.sh</code> script on CGSpace:</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">$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
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Purging 1989 hits from The Knowledge AI in statistics
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Purging 1235 hits from MaCoCu in statistics
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Purging 455 hits from WhatsApp in statistics
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<span style="color:#960050;background-color:#1e0010">
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</span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 3679
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</code></pre></div><h2 id="2021-12-02">2021-12-02</h2>
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<ul>
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<li>Francesca from Alliance asked me for help with approving a submission that gets stuck
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<ul>
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<li>I looked at the PostgreSQL activity and the locks are back up like they were earlier this week</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">$ psql -c <span style="color:#e6db74">"SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
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1
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1 ------------------
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1 (1437 rows)
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1 application_name
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9 psql
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1428 dspaceWeb
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</code></pre></div><ul>
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<li>Munin shows the same:</li>
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</ul>
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<p><img src="/cgspace-notes/2021/12/postgres_locks_ALL-week.png" alt="PostgreSQL locks week"></p>
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<ul>
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<li>Last month I enabled the <code>log_lock_waits</code> in PostgreSQL so I checked the log and was surprised to find only a few since I restarted PostgreSQL three days ago:</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"># grep -E <span style="color:#e6db74">'^2021-(11-29|11-30|12-01|12-02)'</span> /var/log/postgresql/postgresql-10-main.log | grep -c <span style="color:#e6db74">'still waiting for'</span>
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15
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</code></pre></div><ul>
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<li>I think you could analyze the locks for the <code>dspaceWeb</code> user (XMLUI) and find out what queries were locking… but it’s so much information and I don’t know where to start
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<ul>
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<li>For now I just restarted PostgreSQL…</li>
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<li>Francesca was able to do her submission immediately…</li>
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</ul>
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</li>
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<li>On a related note, I want to enable the <code>pg_stat_statement</code> feature to see which queries get run the most, so I created the extension on the CGSpace database</li>
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<li>I was doing some research on PostgreSQL locks and found some interesting things to consider
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<ul>
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<li>The default <code>lock_timeout</code> is 0, aka disabled</li>
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<li>The default <code>statement_timeout</code> is 0, aka disabled</li>
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<li>It seems to be recommended to start by setting <code>statement_timeout</code> first, rule of thumb <a href="https://github.com/jberkus/annotated.conf/blob/master/postgresql.10.simple.conf#L211">ten times longer than your longest query</a></li>
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</ul>
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</li>
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<li>Mark Wood mentioned the <code>checker</code> cron job that apparently runs in one transaction and might be an issue
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<ul>
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<li>I definitely saw it holding a bunch of locks for ~30 minutes during the first part of its execution, then it dropped them and did some other less-intensive things without locks</li>
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</ul>
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</li>
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<li>Bizuwork was still not receiving emails even after we fixed the SMTP access on CGSpace
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<ul>
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<li>After some troubleshooting it turns out that the emails from CGSpace were going in her Junk!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-12-03">2021-12-03</h2>
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<ul>
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<li>I see GARDIAN is now using a “GARDIAN” user agent finally
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<ul>
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<li>I will add them to our local bot override for Solr</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/2021-12/">December, 2021</a></li>
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<li><a href="/cgspace-notes/2021-11/">November, 2021</a></li>
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<li><a href="/cgspace-notes/2021-10/">October, 2021</a></li>
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<li><a href="/cgspace-notes/2021-09/">September, 2021</a></li>
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<li><a href="/cgspace-notes/2021-08/">August, 2021</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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