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310 lines
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310 lines
12 KiB
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<!DOCTYPE html>
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<html lang="en" >
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<head>
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<meta charset="utf-8">
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<meta property="og:title" content="October, 2021" />
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<meta property="og:description" content="2021-10-01
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Export all affiliations on CGSpace and run them against the latest RoR data dump:
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localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", 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;
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$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
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ations-matching.csv
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$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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1879
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$ wc -l /tmp/2021-10-01-affiliations.txt
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7100 /tmp/2021-10-01-affiliations.txt
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So we have 1879/7100 (26.46%) matching already
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-10/" />
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<meta property="article:published_time" content="2021-10-01T11:14:07+03:00" />
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<meta property="article:modified_time" content="2021-10-01T11:14:07+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="October, 2021"/>
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<meta name="twitter:description" content="2021-10-01
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Export all affiliations on CGSpace and run them against the latest RoR data dump:
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localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", 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;
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$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
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ations-matching.csv
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$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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1879
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$ wc -l /tmp/2021-10-01-affiliations.txt
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7100 /tmp/2021-10-01-affiliations.txt
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So we have 1879/7100 (26.46%) matching already
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"/>
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<meta name="generator" content="Hugo 0.88.1" />
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"headline": "October, 2021",
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"url": "https://alanorth.github.io/cgspace-notes/2021-10/",
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"wordCount": "697",
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"datePublished": "2021-10-01T11:14:07+03:00",
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"dateModified": "2021-10-01T11:14:07+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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"keywords": "Notes"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2021-10/">
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<title>October, 2021 | CGSpace Notes</title>
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<link href="https://alanorth.github.io/cgspace-notes/css/style.beb8012edc08ba10be012f079d618dc243812267efe62e11f22fe49618f976a4.css" rel="stylesheet" integrity="sha256-vrgBLtwIuhC+AS8HnWGNwkOBImfv5i4R8i/klhj5dqQ=" crossorigin="anonymous">
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<!-- minified Font Awesome for SVG icons -->
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<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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<div class="container">
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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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<article class="blog-post">
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<header>
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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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<p class="blog-post-meta">
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<time datetime="2021-10-01T11:14:07+03:00">Fri Oct 01, 2021</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-10-01">2021-10-01</h2>
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<ul>
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<li>Export all affiliations on CGSpace and run them against the latest RoR data dump:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", 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;
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$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
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ations-matching.csv
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$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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1879
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$ wc -l /tmp/2021-10-01-affiliations.txt
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7100 /tmp/2021-10-01-affiliations.txt
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</code></pre><ul>
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<li>So we have 1879/7100 (26.46%) matching already</li>
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</ul>
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<h2 id="2021-10-03">2021-10-03</h2>
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<ul>
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<li>Dominique from IWMI asked me for information about how CGSpace partners are using CGSpace APIs to feed their websites</li>
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<li>Start a fresh indexing on AReS</li>
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<li>Udana sent me his file of 292 non-IWMI publications for the Virtual library on water management
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<ul>
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<li>He added licenses</li>
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<li>I want to clean up the <code>dcterms.extent</code> field though because it has volume, issue, and pages there</li>
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<li>I cloned the column several times and extracted values based on their positions, for example:
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<ul>
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<li>Volume: <code>value.partition(":")[0]</code></li>
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<li>Issue: <code>value.partition("(")[2].partition(")")[0]</code></li>
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<li>Page: <code>"p. " + value.replace(".", "")</code></li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-10-04">2021-10-04</h2>
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<ul>
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<li>Start looking at the last month of Solr statistics on CGSpace
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<ul>
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<li>I see a number of IPs with “normal” user agents who clearly behave like bots
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<ul>
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<li>198.15.130.18: 21,000 requests to /discover with a normal-looking user agent, from ASN 11282 (SERVERYOU, US)</li>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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</ul>
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</li>
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<li>Looking closer into the requests with this Mozilla/4.0 user agent, I see 500+ IPs using it:</li>
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</ul>
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</li>
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</ul>
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<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 $1}' | sort | uniq > /tmp/mozilla-4.0-ips.txt
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# wc -l /tmp/mozilla-4.0-ips.txt
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543 /tmp/mozilla-4.0-ips.txt
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</code></pre><ul>
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<li>Then I resolved the IPs and extracted the ones belonging to Amazon:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/resolve-addresses-geoip2.py -i /tmp/mozilla-4.0-ips.txt -k "$ABUSEIPDB_API_KEY" -o /tmp/mozilla-4.0-ips.csv
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$ csvgrep -c asn -m 14618 /tmp/mozilla-4.0-ips.csv | csvcut -c ip | sed 1d | tee /tmp/amazon-ips.txt | wc -l
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</code></pre><ul>
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<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>
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<li>Even more interesting, these requests are weighted VERY heavily on the CGIAR System community:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console"> 1592 GET /handle/10947/2526
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1592 GET /handle/10947/2527
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1592 GET /handle/10947/34
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1593 GET /handle/10947/6
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1594 GET /handle/10947/1
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1598 GET /handle/10947/2515
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1598 GET /handle/10947/2516
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1599 GET /handle/10568/101335
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1599 GET /handle/10568/91688
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1599 GET /handle/10947/2517
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1599 GET /handle/10947/2518
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1599 GET /handle/10947/2519
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1599 GET /handle/10947/2708
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1599 GET /handle/10947/2871
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1600 GET /handle/10568/89342
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1600 GET /handle/10947/4467
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1607 GET /handle/10568/103816
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290382 GET /handle/10568/83389
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</code></pre><ul>
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<li>Before I purge all those I will ask someone Samuel Stacey from the System office to hopefully get an insight…</li>
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<li>Meeting with Michael Victor, Peter, Jane, and Abenet about the future of repositories in the One CGIAR</li>
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<li>Meeting with Michelle from Altmetric about their new CSV upload system
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<ul>
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<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>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-csv" data-lang="csv">doi,handle
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10.1016/j.agsy.2021.103263,10568/115288
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10.3389/fgene.2021.723360,10568/115287
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10.3389/fpls.2021.720670,10568/115285
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</code></pre><ul>
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<li>Extract the AGROVOC subjects from IWMI’s 292 publications to validate them against AGROVOC:</li>
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</ul>
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<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/"//g' | sort -u > /tmp/agrovoc.txt
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$ ./ilri/agrovoc-lookup.py -i /tmp/agrovoc-sorted.txt -o /tmp/agrovoc-matches.csv
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$ csvgrep -c 'number of matches' -m '0' /tmp/agrovoc-matches.csv | csvcut -c 1 > /tmp/invalid-agrovoc.csv
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</code></pre><!-- raw HTML omitted -->
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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/2021-10/">October, 2021</a></li>
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<li><a href="/cgspace-notes/2021-09/">September, 2021</a></li>
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<li><a href="/cgspace-notes/2021-08/">August, 2021</a></li>
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<li><a href="/cgspace-notes/2021-07/">July, 2021</a></li>
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<li><a href="/cgspace-notes/2021-06/">June, 2021</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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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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</p>
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<p>
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<a href="#">Back to top</a>
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</p>
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</footer>
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</body>
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</html>
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