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Atmire merged some changes I had submitted to the COUNTER-Robots project
I updated our local spider user agents and then re-ran the list with my check-spider-hits.sh script on CGSpace:
$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
Purging 1989 hits from The Knowledge AI in statistics
Purging 1235 hits from MaCoCu in statistics
Purging 455 hits from WhatsApp in statistics
Total number of bot hits purged: 3679
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Atmire merged some changes I had submitted to the COUNTER-Robots project
I updated our local spider user agents and then re-ran the list with my check-spider-hits.sh script on CGSpace:
$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
Purging 1989 hits from The Knowledge AI in statistics
Purging 1235 hits from MaCoCu in statistics
Purging 455 hits from WhatsApp in statistics
Total number of bot hits purged: 3679
"/>
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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/2021-12/">December, 2021</a></h2>
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<time datetime="2021-12-01T16:07:07+02:00">Wed Dec 01, 2021</time>
in
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2021-12-01">2021-12-01</h2>
<ul>
<li>Atmire merged some changes I had submitted to the COUNTER-Robots project</li>
<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>
</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">$ ./ilri/check-spider-hits.sh -f /tmp/agents -p
Purging 1989 hits from The Knowledge AI in statistics
Purging 1235 hits from MaCoCu in statistics
Purging 455 hits from WhatsApp in statistics
<span style="color:#960050;background-color:#1e0010">
</span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 3679
</code></pre></div><h2 id="2021-12-02">2021-12-02</h2>
<ul>
<li>Francesca from Alliance asked me for help with approving a submission that gets stuck
<ul>
<li>I looked at the PostgreSQL activity and the locks are back up like they were earlier this week</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">$ 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
1
1 ------------------
1 (1437 rows)
1 application_name
9 psql
1428 dspaceWeb
</code></pre></div><ul>
<li>Munin shows the same:</li>
</ul>
<p><img src="/cgspace-notes/2021/12/postgres_locks_ALL-week.png" alt="PostgreSQL locks week"></p>
<ul>
<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>
</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"># 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>
15
</code></pre></div><ul>
<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
<ul>
<li>For now I just restarted PostgreSQL…</li>
<li>Francesca was able to do her submission immediately…</li>
</ul>
</li>
<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>
<li>I was doing some research on PostgreSQL locks and found some interesting things to consider
<ul>
<li>The default <code>lock_timeout</code> is 0, aka disabled</li>
<li>The default <code>statement_timeout</code> is 0, aka disabled</li>
<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>
</ul>
</li>
<li>Mark Wood mentioned the <code>checker</code> cron job that apparently runs in one transaction and might be an issue
<ul>
<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>
</ul>
</li>
<li>Bizuwork was still not receiving emails even after we fixed the SMTP access on CGSpace
<ul>
<li>After some troubleshooting it turns out that the emails from CGSpace were going in her Junk!</li>
</ul>
</li>
</ul>
<h2 id="2021-12-03">2021-12-03</h2>
<ul>
<li>I see GARDIAN is now using a “GARDIAN” user agent finally
<ul>
<li>I will add them to our local spider agent override in DSpace so that the hits don’t get counted in Solr</li>
</ul>
</li>
</ul>
<h2 id="2021-12-05">2021-12-05</h2>
<ul>
<li>Proof fifty records Abenet sent me from Africa Rice Center (“AfricaRice 1st batch Import”)
<ul>
<li>Fixed forty-six incorrect collections</li>
<li>Cleaned up and normalize affiliations</li>
<li>Cleaned up dates (extra <code>*</code> character in all?)</li>
<li>Cleaned up citation format</li>
<li>Fixed some encoding issues in abstracts</li>
<li>Removed empty columns</li>
<li>Removed one duplicate: Enhancing Rice Productivity and Soil Nitrogen Using Dual-Purpose Cowpea-NERICA® Rice Sequence in Degraded Savanna</li>
<li>Added volume and issue metadata by extracting it from the citations</li>
<li>All PDFs hosted on davidpublishing.com are dead…</li>
<li>All DOIs linking to African Journal of Agricultural Research are dead…</li>
<li>Fixed a handful of items marked as “Open Access” that are actually closed</li>
<li>Added many missing ISSNs</li>
<li>Added many missing countries/regions</li>
<li>Fixed invalid AGROVOC terms and added some more based on article subjects</li>
</ul>
</li>
<li>I also made some minor changes to the <a href="https://github.com/ilri/csv-metadata-quality">CSV Metadata Quality Checker</a>
<ul>
<li>Added the ability to check if the item’s title exists in the citation</li>
<li>Updated to only run the mojibake check if we’re not running in unsafe mode (so we don’t print the same warning during both the check and fix steps)</li>
</ul>
</li>
<li>I ran the re-harvesting on AReS</li>
</ul>
<h2 id="2021-12-06">2021-12-06</h2>
<ul>
<li>Some minor work on the <code>check-duplicates.py</code> script I wrote last month
<ul>
<li>I found some corner cases where there were items that matched in the database, but they were <code>in_archive=f</code> and or <code>withdrawn=t</code> so I check that before trying to resolve the handles of potential duplicates</li>
</ul>
</li>
<li>More work on the Africa Rice Center 1st batch import
<ul>
<li>I merged the metadata for three duplicates in Africa Rice’s items and mapped them on CGSpace</li>
<li>I did a bit more work to add missing AGROVOC subjects, countries, regions, extents, etc and then uploaded the forty-six items to CGSpace</li>
</ul>
</li>
<li>I started looking at the seventy CAS records that Abenet has been working on for the past few months</li>
</ul>
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<ol class="list-unstyled">
<li><a href="/cgspace-notes/2021-12/">December, 2021</a></li>
<li><a href="/cgspace-notes/2021-11/">November, 2021</a></li>
<li><a href="/cgspace-notes/2021-10/">October, 2021</a></li>
<li><a href="/cgspace-notes/2021-09/">September, 2021</a></li>
<li><a href="/cgspace-notes/2021-08/">August, 2021</a></li>
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