mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-23 05:32:20 +01:00
314 lines
12 KiB
HTML
314 lines
12 KiB
HTML
<!DOCTYPE html>
|
|
<html lang="en" >
|
|
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
|
|
|
|
|
<meta property="og:title" content="December, 2021" />
|
|
<meta property="og:description" content="2021-12-01
|
|
|
|
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
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-12/" />
|
|
<meta property="article:published_time" content="2021-12-01T16:07:07+02:00" />
|
|
<meta property="article:modified_time" content="2021-12-05T17:55:47+02:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="December, 2021"/>
|
|
<meta name="twitter:description" content="2021-12-01
|
|
|
|
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
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.89.4" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "December, 2021",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2021-12/",
|
|
"wordCount": "711",
|
|
"datePublished": "2021-12-01T16:07:07+02:00",
|
|
"dateModified": "2021-12-05T17:55:47+02:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2021-12/">
|
|
|
|
<title>December, 2021 | CGSpace Notes</title>
|
|
|
|
|
|
<!-- combined, minified CSS -->
|
|
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.beb8012edc08ba10be012f079d618dc243812267efe62e11f22fe49618f976a4.css" rel="stylesheet" integrity="sha256-vrgBLtwIuhC+AS8HnWGNwkOBImfv5i4R8i/klhj5dqQ=" crossorigin="anonymous">
|
|
|
|
|
|
<!-- minified Font Awesome for SVG icons -->
|
|
|
|
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
|
|
|
|
<!-- RSS 2.0 feed -->
|
|
|
|
|
|
|
|
|
|
</head>
|
|
|
|
<body>
|
|
|
|
|
|
<div class="blog-masthead">
|
|
<div class="container">
|
|
<nav class="nav blog-nav">
|
|
<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
|
|
</nav>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
|
|
|
|
<header class="blog-header">
|
|
<div class="container">
|
|
<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>
|
|
</div>
|
|
</header>
|
|
|
|
|
|
|
|
|
|
<div class="container">
|
|
<div class="row">
|
|
<div class="col-sm-8 blog-main">
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-12/">December, 2021</a></h2>
|
|
<p class="blog-post-meta">
|
|
<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>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<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>
|
|
<!-- raw HTML omitted -->
|
|
|
|
|
|
|
|
|
|
|
|
</article>
|
|
|
|
|
|
|
|
</div> <!-- /.blog-main -->
|
|
|
|
<aside class="col-sm-3 ml-auto blog-sidebar">
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<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>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<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>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
</aside>
|
|
|
|
|
|
</div> <!-- /.row -->
|
|
</div> <!-- /.container -->
|
|
|
|
|
|
|
|
<footer class="blog-footer">
|
|
<p dir="auto">
|
|
|
|
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
|
|
|
</p>
|
|
<p>
|
|
<a href="#">Back to top</a>
|
|
</p>
|
|
</footer>
|
|
|
|
|
|
</body>
|
|
|
|
</html>
|