cgspace-notes/docs/2021-10/index.html
2021-10-04 19:40:13 +03:00

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Export all affiliations on CGSpace and run them against the latest RoR data dump:
localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;cg.contributor.affiliation&quot;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d &gt; /tmp/2021-10-01-affiliations.txt
$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
ations-matching.csv
$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
1879
$ wc -l /tmp/2021-10-01-affiliations.txt
7100 /tmp/2021-10-01-affiliations.txt
So we have 1879/7100 (26.46%) matching already
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<meta name="twitter:title" content="October, 2021"/>
<meta name="twitter:description" content="2021-10-01
Export all affiliations on CGSpace and run them against the latest RoR data dump:
localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;cg.contributor.affiliation&quot;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d &gt; /tmp/2021-10-01-affiliations.txt
$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
ations-matching.csv
$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
1879
$ wc -l /tmp/2021-10-01-affiliations.txt
7100 /tmp/2021-10-01-affiliations.txt
So we have 1879/7100 (26.46%) matching already
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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/2021-10/">October, 2021</a></h2>
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<time datetime="2021-10-01T11:14:07+03:00">Fri Oct 01, 2021</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2021-10-01">2021-10-01</h2>
<ul>
<li>Export all affiliations on CGSpace and run them against the latest RoR data dump:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;cg.contributor.affiliation&quot;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d &gt; /tmp/2021-10-01-affiliations.txt
$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
ations-matching.csv
$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
1879
$ wc -l /tmp/2021-10-01-affiliations.txt
7100 /tmp/2021-10-01-affiliations.txt
</code></pre><ul>
<li>So we have 1879/7100 (26.46%) matching already</li>
</ul>
<h2 id="2021-10-03">2021-10-03</h2>
<ul>
<li>Dominique from IWMI asked me for information about how CGSpace partners are using CGSpace APIs to feed their websites</li>
<li>Start a fresh indexing on AReS</li>
<li>Udana sent me his file of 292 non-IWMI publications for the Virtual library on water management
<ul>
<li>He added licenses</li>
<li>I want to clean up the <code>dcterms.extent</code> field though because it has volume, issue, and pages there</li>
<li>I cloned the column several times and extracted values based on their positions, for example:
<ul>
<li>Volume: <code>value.partition(&quot;:&quot;)[0]</code></li>
<li>Issue: <code>value.partition(&quot;(&quot;)[2].partition(&quot;)&quot;)[0]</code></li>
<li>Page: <code>&quot;p. &quot; + value.replace(&quot;.&quot;, &quot;&quot;)</code></li>
</ul>
</li>
</ul>
</li>
</ul>
<h2 id="2021-10-04">2021-10-04</h2>
<ul>
<li>Start looking at the last month of Solr statistics on CGSpace
<ul>
<li>I see a number of IPs with &ldquo;normal&rdquo; user agents who clearly behave like bots
<ul>
<li>198.15.130.18: 21,000 requests to /discover with a normal-looking user agent, from ASN 11282 (SERVERYOU, US)</li>
<li>93.158.90.107: 8,500 requests to handle and browse links with a Firefox 84.0 user agent, from ASN 12552 (IPO-EU, SE)</li>
<li>193.235.141.162: 4,800 requests to handle, browse, and discovery links with a Firefox 84.0 user agent, from ASN 51747 (INTERNETBOLAGET, SE)</li>
<li>3.225.28.105: 2,900 requests to REST API for the CIAT Story Maps collection with a normal user agent, from ASN 14618 (AMAZON-AES, US)</li>
<li>34.228.236.6: 2,800 requests to discovery for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
<li>18.212.137.2: 2,800 requests to discovery for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
<li>3.81.123.72: 2,800 requests to discovery and handles for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
<li>3.227.16.188: 2,800 requests to discovery and handles for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
</ul>
</li>
<li>Looking closer into the requests with this Mozilla/4.0 user agent, I see 500+ IPs using it:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"># zcat --force /var/log/nginx/*.log* | grep 'Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)' | awk '{print $1}' | sort | uniq &gt; /tmp/mozilla-4.0-ips.txt
# wc -l /tmp/mozilla-4.0-ips.txt
543 /tmp/mozilla-4.0-ips.txt
</code></pre><ul>
<li>Then I resolved the IPs and extracted the ones belonging to Amazon:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/resolve-addresses-geoip2.py -i /tmp/mozilla-4.0-ips.txt -k &quot;$ABUSEIPDB_API_KEY&quot; -o /tmp/mozilla-4.0-ips.csv
$ csvgrep -c asn -m 14618 /tmp/mozilla-4.0-ips.csv | csvcut -c ip | sed 1d | tee /tmp/amazon-ips.txt | wc -l
</code></pre><ul>
<li>I am thinking I will purge them all, as I have several indicators that they are bots: mysterious user agent, IP owned by Amazon</li>
<li>Even more interesting, these requests are weighted VERY heavily on the CGIAR System community:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console"> 1592 GET /handle/10947/2526
1592 GET /handle/10947/2527
1592 GET /handle/10947/34
1593 GET /handle/10947/6
1594 GET /handle/10947/1
1598 GET /handle/10947/2515
1598 GET /handle/10947/2516
1599 GET /handle/10568/101335
1599 GET /handle/10568/91688
1599 GET /handle/10947/2517
1599 GET /handle/10947/2518
1599 GET /handle/10947/2519
1599 GET /handle/10947/2708
1599 GET /handle/10947/2871
1600 GET /handle/10568/89342
1600 GET /handle/10947/4467
1607 GET /handle/10568/103816
290382 GET /handle/10568/83389
</code></pre><ul>
<li>Before I purge all those I will ask someone Samuel Stacey from the System office to hopefully get an insight&hellip;</li>
<li>Meeting with Michael Victor, Peter, Jane, and Abenet about the future of repositories in the One CGIAR</li>
<li>Meeting with Michelle from Altmetric about their new CSV upload system
<ul>
<li>I sent her some examples of Handles that have DOIs, but no linked score (yet) to see if an association will be created when she uploads them</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-csv" data-lang="csv">doi,handle
10.1016/j.agsy.2021.103263,10568/115288
10.3389/fgene.2021.723360,10568/115287
10.3389/fpls.2021.720670,10568/115285
</code></pre><ul>
<li>Extract the AGROVOC subjects from IWMI&rsquo;s 292 publications to validate them against AGROVOC:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -c 'dcterms.subject[en_US]' ~/Downloads/2021-10-03-non-IWMI-publications.csv | sed -e 1d -e 's/||/\n/g' -e 's/&quot;//g' | sort -u &gt; /tmp/agrovoc.txt
$ ./ilri/agrovoc-lookup.py -i /tmp/agrovoc-sorted.txt -o /tmp/agrovoc-matches.csv
$ csvgrep -c 'number of matches' -m '0' /tmp/agrovoc-matches.csv | csvcut -c 1 &gt; /tmp/invalid-agrovoc.csv
</code></pre><!-- raw HTML omitted -->
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<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>
<li><a href="/cgspace-notes/2021-07/">July, 2021</a></li>
<li><a href="/cgspace-notes/2021-06/">June, 2021</a></li>
</ol>
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<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>
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