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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/2023-12/">December, 2023</a></h2>
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<time datetime="2023-12-01T08:48:36+03:00">Fri Dec 01, 2023</time>
in
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2023-12-01">2023-12-01</h2>
<ul>
<li>There is still high load on CGSpace and I don’t know why
<ul>
<li>I don’t see a high number of sessions compared to previous days in the last few weeks</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
<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>$ <span style="color:#66d9ef">for</span> file in dspace.log.2023-11-<span style="color:#f92672">[</span>23<span style="color:#f92672">]</span>*; <span style="color:#66d9ef">do</span> echo <span style="color:#e6db74">"</span>$file<span style="color:#e6db74">"</span>; grep -a -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}'</span> <span style="color:#e6db74">"</span>$file<span style="color:#e6db74">"</span> | sort | uniq | wc -l; <span style="color:#66d9ef">done</span>
</span></span><span style="display:flex;"><span>dspace.log.2023-11-20
</span></span><span style="display:flex;"><span>22865
</span></span><span style="display:flex;"><span>dspace.log.2023-11-21
</span></span><span style="display:flex;"><span>20296
</span></span><span style="display:flex;"><span>dspace.log.2023-11-22
</span></span><span style="display:flex;"><span>19688
</span></span><span style="display:flex;"><span>dspace.log.2023-11-23
</span></span><span style="display:flex;"><span>17906
</span></span><span style="display:flex;"><span>dspace.log.2023-11-24
</span></span><span style="display:flex;"><span>18453
</span></span><span style="display:flex;"><span>dspace.log.2023-11-25
</span></span><span style="display:flex;"><span>17513
</span></span><span style="display:flex;"><span>dspace.log.2023-11-26
</span></span><span style="display:flex;"><span>19037
</span></span><span style="display:flex;"><span>dspace.log.2023-11-27
</span></span><span style="display:flex;"><span>21103
</span></span><span style="display:flex;"><span>dspace.log.2023-11-28
</span></span><span style="display:flex;"><span>23023
</span></span><span style="display:flex;"><span>dspace.log.2023-11-29
</span></span><span style="display:flex;"><span>23545
</span></span><span style="display:flex;"><span>dspace.log.2023-11-30
</span></span><span style="display:flex;"><span>21298
</span></span></code></pre></div><ul>
<li>Even the number of unique IPs is not very high compared to the last week or so:</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># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.1 | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>17023
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.2.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>17294
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.3.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>22057
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.4.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>32956
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.5.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>11415
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.6.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>15444
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.7.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>12648
</span></span></code></pre></div><ul>
<li>It doesn’t make any sense so I think I’m going to restart the server…
<ul>
<li>After restarting the server the load went down to normal levels… who knows…</li>
</ul>
</li>
<li>I started trying to see how I’m going to generate the fake statistics for the Alliance bitstream that was replaced
<ul>
<li>I exported all the statistics for the owningItem now:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/stats-export.json -f <span style="color:#e6db74">'owningItem:b5862bfa-9799-4167-b1cf-76f0f4ea1e18'</span> -k uid
</span></span></code></pre></div><ul>
<li>Importing them into DSpace Test didn’t show the statistics in the Atmire module, but I see them in Solr…</li>
</ul>
<h2 id="2023-12-02">2023-12-02</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-12-04">2023-12-04</h2>
<ul>
<li>Send a message to Altmetric support because the item IWMI highlighted last month still doesn’t show the attention score for the Handle after I tweeted it several times weeks ago</li>
<li>Spent some time writing a Python script to fix the literal MaxMind City JSON objects in our Solr statistics
<ul>
<li>There are about 1.6 million of these, so I exported them using solr-import-export-json with the query <code>city:com*</code> but ended up finding many that have missing bundles, container bitstreams, etc:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>city:com* AND -bundleName:[* TO *] AND -containerBitstream:[* TO *] AND -file_id:[* TO *] AND -owningItem:[* TO *] AND -version_id:[* TO *]
</code></pre><ul>
<li>(Note the negation to find fields that are missing)</li>
<li>I don’t know what I want to do with these yet</li>
</ul>
<h2 id="2023-12-05">2023-12-05</h2>
<ul>
<li>I finished the <code>fix_maxmind_stats.py</code> script and fixed 1.6 million records and imported them on CGSpace after testing on DSpace 7 Test</li>
<li>Altmetric said there was a glitch regarding the Handle and DOI linking and they successfully re-scraped the item page and linked them
<ul>
<li>They sent me a list of current production IPs and I notice that some of them are in our nginx bot network list:</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"><span style="display:flex;"><span>$ <span style="color:#66d9ef">for</span> network in <span style="color:#66d9ef">$(</span>csvcut -c network /tmp/ips.csv | sed 1d | sort -u<span style="color:#66d9ef">)</span>; <span style="color:#66d9ef">do</span> grepcidr $network ~/src/git/rmg-ansible-public/roles/dspace/files/nginx/bot-networks.conf; <span style="color:#66d9ef">done</span>
</span></span><span style="display:flex;"><span>108.128.0.0/13 'bot';
</span></span><span style="display:flex;"><span>46.137.0.0/16 'bot';
</span></span><span style="display:flex;"><span>52.208.0.0/13 'bot';
</span></span><span style="display:flex;"><span>52.48.0.0/13 'bot';
</span></span><span style="display:flex;"><span>54.194.0.0/15 'bot';
</span></span><span style="display:flex;"><span>54.216.0.0/14 'bot';
</span></span><span style="display:flex;"><span>54.220.0.0/15 'bot';
</span></span><span style="display:flex;"><span>54.228.0.0/15 'bot';
</span></span><span style="display:flex;"><span>63.32.242.35/32 'bot';
</span></span><span style="display:flex;"><span>63.32.0.0/14 'bot';
</span></span><span style="display:flex;"><span>99.80.0.0/15 'bot'
</span></span></code></pre></div><ul>
<li>I will remove those for now so that Altmetric doesn’t have any unexpected issues harvesting</li>
</ul>
<h2 id="2023-12-08">2023-12-08</h2>
<ul>
<li>Finalized the script to generate Solr statistics for Alliance research Mirjam
<ul>
<li>The script is <code>ilri/generate_solr_statistics.py</code></li>
<li>I generated ~3,200 statistics based on her records of the download statistics of <a href="https://hdl.handle.net/10568/131997">that item</a> and imported them on CGSpace</li>
</ul>
</li>
<li>Did some work on the DSpace 7 submission form</li>
<li>Peter asked for lists of affiliations, investors, and publishers to do some cleanups
<ul>
<li>I generated a list from a CSV export instead of doing it based on a SQL dump…</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'cg.contributor.affiliation[en_US]'</span> /tmp/initiatives.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | sed -e 1d -e 's/^"//' -e 's/"$//' -e 's/||/\n/g' -e '/^$/d' \
</span></span><span style="display:flex;"><span> | sort | uniq -c | sort -hr \
</span></span><span style="display:flex;"><span> | awk 'BEGIN { FS = "^[[:space:]]+[[:digit:]]+[[:space:]]+" } {print $2}'\
</span></span><span style="display:flex;"><span> | sed -e '1i cg.contributor.affiliation' -e 's/^\(.*\)$/"\1"/' \
</span></span><span style="display:flex;"><span> > /tmp/2023-12-08-initiatives-affiliations.csv
</span></span></code></pre></div><ul>
<li>Export a list of authors as well:</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>localhost/dspace7= ☘ \COPY (SELECT DISTINCT text_value AS "dc.contributor.author", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 3 GROUP BY "dc.contributor.author" ORDER BY count DESC) to /tmp/2023-12-08-authors.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>COPY 102435
</span></span></code></pre></div><h2 id="2023-12-11">2023-12-11</h2>
<ul>
<li>Work on OpenRXV dependencies and podman a bit</li>
<li>Peter noticed that the statistics for this month are very very low on CGSpace
<ul>
<li>I don’t know what is going on, perhaps it is related to me adjusting the nginx config last week?</li>
<li>Ah, it’s probably because of the spider patterns I updated on 2023-11</li>
</ul>
</li>
</ul>
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<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
<li><a href="/cgspace-notes/2023-11/">November, 2023</a></li>
<li><a href="/cgspace-notes/2023-10/">October, 2023</a></li>
<li><a href="/cgspace-notes/2023-09/">September, 2023</a></li>
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