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<meta property="og:title" content="October, 2024" />
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<meta property="og:description" content="2024-10-03
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I had an idea to get abstracts from OpenAlex
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For copyright reasons they don’t include plain abstracts, but the pyalex library can convert them on the fly
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" />
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<meta name="twitter:title" content="October, 2024"/>
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<meta name="twitter:description" content="2024-10-03
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I had an idea to get abstracts from OpenAlex
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For copyright reasons they don’t include plain abstracts, but the pyalex library can convert them on the fly
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"/>
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"headline": "October, 2024",
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<title>October, 2024 | 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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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-10/">October, 2024</a></h2>
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<p class="blog-post-meta">
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<time datetime="2024-10-03T11:01:00+03:00">Thu Oct 03, 2024</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2024-10-03">2024-10-03</h2>
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<ul>
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<li>I had an idea to get abstracts from OpenAlex
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<ul>
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<li>For <a href="https://docs.openalex.org/api-entities/works/work-object#abstract_inverted_index">copyright reasons they don’t include plain abstracts</a>, but the <a href="https://github.com/J535D165/pyalex">pyalex</a> library can convert them on the fly</li>
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</ul>
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</li>
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</ul>
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<ul>
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<li>I filtered for journal articles that were Creative Commons and missing abstracts:</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"><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'id,dc.title[en_US],dcterms.abstract[en_US],cg.identifier.doi[en_US],dcterms.type[en_US],dcterms.language[en_US],dcterms.license[en_US]'</span> ~/Downloads/2024-09-30-cgspace.csv | csvgrep -c <span style="color:#e6db74">'dcterms.type[en_US]'</span> -r <span style="color:#e6db74">'^Journal Article$'</span> | csvgrep -c <span style="color:#e6db74">'cg.identifier.doi[en_US]'</span> -r <span style="color:#e6db74">'^.+$'</span> | csvgrep -c <span style="color:#e6db74">'dcterms.license[en_US]'</span> -r <span style="color:#e6db74">'^CC-'</span> | csvgrep -c <span style="color:#e6db74">'dcterms.abstract[en_US]'</span> -r <span style="color:#e6db74">'^$'</span> | csvgrep -c <span style="color:#e6db74">'dcterms.language[en_US]'</span> -r <span style="color:#e6db74">'^en$'</span> | grep -v <span style="color:#e6db74">"||"</span> | grep -v -- <span style="color:#e6db74">'-ND'</span> | grep -v -E <span style="color:#e6db74">'https://doi.org/10.(2499|4160|17528)/'</span> > /tmp/missing-abstracts.csv
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</span></span></code></pre></div><ul>
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<li>Then wrote a script to get them from OpenAlex
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<ul>
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<li>After inspecting and cleaning a few dozen up in OpenRefine (removing “Keywords:” and copyright, and HTML entities, etc) I managed to get about 440</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-10-06">2024-10-06</h2>
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<ul>
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<li>Since I increase Solr’s heap from 2 to 3G a few weeks ago it seems like Solr is always using 100% CPU
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<ul>
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<li>I don’t understand this because it was running well before, and I only increased it in anticipation of running the dspace-statistics-api-js, though never got around to it</li>
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<li>I just realized that this may be related to the JMX monitoring, as I’ve seen gaps in the Grafana dashboards and remember that it took surprisingly long to scrape the metrics</li>
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<li>Maybe I need to change the scrape interval</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-10-08">2024-10-08</h2>
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<ul>
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<li>I checked the VictoriaMetrics vmagent dashboard and saw that there were thousands of errors scraping the <code>jvm_solr</code> target from Solr
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<ul>
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<li>So it seems like I do need to change the scrape interval</li>
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<li>I will increase it from 15s (global) to 20s for that job</li>
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<li>Reading some documentation I found <a href="https://www.robustperception.io/keep-it-simple-scrape_interval-id/">this reference from Brian Brazil that discusses this very problem</a></li>
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<li>He recommends keeping a single scrape interval for all targets, but also checking the slow exporter (<code>jmx_exporter</code> in this case) and seeing if we can limit the data we scrape</li>
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<li>To keep things simple for now I will increase the global scrape interval to 20s</li>
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<li>Long term I should limit the metrics…</li>
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<li>Oh wow, I found out that <a href="https://solr.apache.org/guide/8_11/monitoring-solr-with-prometheus-and-grafana.html">Solr ships with a Prometheus exporter!</a> and even includes a Grafana dashboard</li>
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</ul>
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</li>
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<li>I’m trying to run the Solr prometheus-exporter as a one-off systemd unit to test it:</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"><span style="display:flex;"><span># cd /opt/solr-8.11.3/contrib/prometheus-exporter
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</span></span><span style="display:flex;"><span># systemd-run --uid<span style="color:#f92672">=</span>victoriametrics --gid<span style="color:#f92672">=</span>victoriametrics --working-directory<span style="color:#f92672">=</span>/opt/solr-8.11.3/contrib/prometheus-exporter ./bin/solr-exporter -p <span style="color:#ae81ff">9854</span> -b http://localhost:8983/solr -f ./conf/solr-exporter-config.xml -s <span style="color:#ae81ff">20</span>
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</span></span></code></pre></div><ul>
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<li>The default scrape interval is 60 seconds, so if we scrape it more than that the metrics will be stale
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<ul>
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<li>From what I’ve seen this returns in less than one second so it should be safe to reduce the scrape interval</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/2024-10/">October, 2024</a></li>
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<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
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<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
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<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
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<li><a href="/cgspace-notes/2024-06/">June, 2024</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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