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<meta property="og:description" content="2018-11-01
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Finalize AReS Phase I and Phase II ToRs
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Send a note about my dspace-statistics-api to the dspace-tech mailing list
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2018-11-03
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Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
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Today these are the top 10 IPs:
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<meta name="twitter:title" content="November, 2018"/>
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<meta name="twitter:description" content="2018-11-01
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Finalize AReS Phase I and Phase II ToRs
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Send a note about my dspace-statistics-api to the dspace-tech mailing list
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2018-11-03
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Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
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Today these are the top 10 IPs:
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-11/">November, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-11-01T16:41:30+02:00">Thu Nov 01, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-11-01">2018-11-01</h2>
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<ul>
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<li>Finalize AReS Phase I and Phase II ToRs</li>
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<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
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</ul>
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<h2 id="2018-11-03">2018-11-03</h2>
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<ul>
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<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
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<li>Today these are the top 10 IPs:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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1300 66.249.64.63
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1384 35.237.175.180
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1430 138.201.52.218
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1455 207.46.13.156
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1500 40.77.167.175
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1979 50.116.102.77
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2790 66.249.64.61
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3367 84.38.130.177
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4537 70.32.83.92
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22508 66.249.64.59
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</code></pre>
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<ul>
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<li>The <code>66.249.64.x</code> are definitely Google</li>
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<li><code>70.32.83.92</code> is well known, probably CCAFS or something, as it’s only a few thousand requests and always to REST API</li>
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<li><code>84.38.130.177</code> is some new IP in Latvia that is only hitting the XMLUI, using the following user agent:</li>
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</ul>
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<pre><code>Mozilla/5.0 (Windows NT 5.1) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.792.0 Safari/535.1
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</code></pre>
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<ul>
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<li>They at least seem to be re-using their Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=84.38.130.177' dspace.log.2018-11-03 | sort | uniq
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342
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</code></pre>
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<ul>
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<li><code>50.116.102.77</code> is also a regular REST API user</li>
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<li><code>40.77.167.175</code> and <code>207.46.13.156</code> seem to be Bing</li>
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<li><code>138.201.52.218</code> seems to be on Hetzner in Germany, but is using this user agent:</li>
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</ul>
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<pre><code>Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0
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</code></pre>
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<ul>
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<li>And it doesn’t seem they are re-using their Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=138.201.52.218' dspace.log.2018-11-03 | sort | uniq
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1243
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</code></pre>
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<ul>
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<li>Ah, we’ve apparently seen this server exactly a year ago in 2017-11, making 40,000 requests in one day…</li>
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<li>I wonder if it’s worth adding them to the list of bots in the nginx config?</li>
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<li>Linode sent a mail that CGSpace (linode18) is using high outgoing bandwidth</li>
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<li>Looking at the nginx logs again I see the following top ten IPs:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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1979 50.116.102.77
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1980 35.237.175.180
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2186 207.46.13.156
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2208 40.77.167.175
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2843 66.249.64.63
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4220 84.38.130.177
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4537 70.32.83.92
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5593 66.249.64.61
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12557 78.46.89.18
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32152 66.249.64.59
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</code></pre>
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<ul>
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<li><code>78.46.89.18</code> is new since I last checked a few hours ago, and it’s from Hetzner with the following user agent:</li>
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</ul>
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<pre><code>Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0
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</code></pre>
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<ul>
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<li>It’s making lots of requests and using quite a number of Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=78.46.89.18' /home/cgspace.cgiar.org/log/dspace.log.2018-11-03 | sort | uniq
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8449
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</code></pre>
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<ul>
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<li>I could add this IP to the list of bot IPs in nginx, but it seems like a futile effort when some new IP could come along and do the same thing</li>
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<li>Perhaps I should think about adding rate limits to dynamic pages like <code>/discover</code> and <code>/browse</code></li>
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<li>I think it’s reasonable for a human to click one of those links five or ten times a minute…</li>
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<li>To contrast, <code>78.46.89.18</code> made about 300 requests per minute for a few hours today:</li>
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</ul>
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<pre><code># grep 78.46.89.18 /var/log/nginx/access.log | grep -o -E '03/Nov/2018:[0-9][0-9]:[0-9][0-9]' | sort | uniq -c | sort -n | tail -n 20
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286 03/Nov/2018:18:02
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287 03/Nov/2018:18:21
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289 03/Nov/2018:18:23
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291 03/Nov/2018:18:27
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293 03/Nov/2018:18:34
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300 03/Nov/2018:17:58
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300 03/Nov/2018:18:22
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300 03/Nov/2018:18:32
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304 03/Nov/2018:18:12
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305 03/Nov/2018:18:13
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305 03/Nov/2018:18:24
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312 03/Nov/2018:18:39
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322 03/Nov/2018:18:17
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326 03/Nov/2018:18:38
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327 03/Nov/2018:18:16
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330 03/Nov/2018:17:57
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332 03/Nov/2018:18:19
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336 03/Nov/2018:17:56
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340 03/Nov/2018:18:14
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341 03/Nov/2018:18:18
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</code></pre>
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<ul>
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<li>If they want to download all our metadata and PDFs they should use an API rather than scraping the XMLUI</li>
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<li>I will add them to the list of bot IPs in nginx for now and think about enforcing rate limits in XMLUI later</li>
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<li>Also, this is the third (?) time a mysterious IP on Hetzner has done this… who is this?</li>
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</ul>
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<h2 id="2018-11-04">2018-11-04</h2>
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<ul>
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<li>Forward Peter’s information about CGSpace financials to Modi from ICRISAT</li>
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<li>Linode emailed about the CPU load and outgoing bandwidth on CGSpace (linode18) again</li>
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<li>Here are the top ten IPs active so far this morning:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "04/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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1083 2a03:2880:11ff:2::face:b00c
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1105 2a03:2880:11ff:d::face:b00c
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1111 2a03:2880:11ff:f::face:b00c
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1134 84.38.130.177
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1893 50.116.102.77
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2040 66.249.64.63
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4210 66.249.64.61
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4534 70.32.83.92
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13036 78.46.89.18
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20407 66.249.64.59
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</code></pre>
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<ul>
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<li><code>78.46.89.18</code> is back… and still making tons of Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=78.46.89.18' dspace.log.2018-11-04 | sort | uniq
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8765
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</code></pre>
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<ul>
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<li>Also, now we have a ton of Facebook crawlers:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "04/Nov/2018" | grep "2a03:2880:11ff:" | awk '{print $1}' | sort | uniq -c | sort -n
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905 2a03:2880:11ff:b::face:b00c
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955 2a03:2880:11ff:5::face:b00c
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965 2a03:2880:11ff:e::face:b00c
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984 2a03:2880:11ff:8::face:b00c
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993 2a03:2880:11ff:3::face:b00c
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994 2a03:2880:11ff:7::face:b00c
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1006 2a03:2880:11ff:10::face:b00c
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1011 2a03:2880:11ff:4::face:b00c
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1023 2a03:2880:11ff:6::face:b00c
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1026 2a03:2880:11ff:9::face:b00c
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1039 2a03:2880:11ff:1::face:b00c
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1043 2a03:2880:11ff:c::face:b00c
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1070 2a03:2880:11ff::face:b00c
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1075 2a03:2880:11ff:a::face:b00c
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1093 2a03:2880:11ff:2::face:b00c
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1107 2a03:2880:11ff:d::face:b00c
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1116 2a03:2880:11ff:f::face:b00c
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</code></pre>
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<ul>
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<li>They are really making shit tons of Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a03:2880:11ff' dspace.log.2018-11-04 | sort | uniq
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14368
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</code></pre>
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<ul>
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<li>Their user agent is:</li>
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</ul>
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<pre><code>facebookexternalhit/1.1 (+http://www.facebook.com/externalhit_uatext.php)
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</code></pre>
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<ul>
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<li>I will add it to the Tomcat Crawler Session Manager valve</li>
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<li>Later in the evening… ok, this Facebook bot is getting super annoying:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "04/Nov/2018" | grep "2a03:2880:11ff:" | awk '{print $1}' | sort | uniq -c | sort -n
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1871 2a03:2880:11ff:3::face:b00c
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1885 2a03:2880:11ff:b::face:b00c
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1941 2a03:2880:11ff:8::face:b00c
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1942 2a03:2880:11ff:e::face:b00c
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1987 2a03:2880:11ff:1::face:b00c
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2023 2a03:2880:11ff:2::face:b00c
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2027 2a03:2880:11ff:4::face:b00c
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2032 2a03:2880:11ff:9::face:b00c
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2034 2a03:2880:11ff:10::face:b00c
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2050 2a03:2880:11ff:5::face:b00c
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2061 2a03:2880:11ff:c::face:b00c
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2076 2a03:2880:11ff:6::face:b00c
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2093 2a03:2880:11ff:7::face:b00c
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2107 2a03:2880:11ff::face:b00c
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2118 2a03:2880:11ff:d::face:b00c
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2164 2a03:2880:11ff:a::face:b00c
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2178 2a03:2880:11ff:f::face:b00c
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</code></pre>
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<ul>
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<li>And still making shit tons of Tomcat sessions:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a03:2880:11ff' dspace.log.2018-11-04 | sort | uniq
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28470
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</code></pre>
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<ul>
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<li>And that’s even using the Tomcat Crawler Session Manager valve!</li>
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<li>Maybe we need to limit more dynamic pages, like the “most popular” country, item, and author pages</li>
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<li>It seems these are popular too, and there is no fucking way Facebook needs that information, yet they are requesting thousands of them!</li>
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</ul>
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<pre><code># grep 'face:b00c' /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -c 'most-popular/'
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7033
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</code></pre>
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<ul>
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<li>I added the “most-popular” pages to the list that return <code>X-Robots-Tag: none</code> to try to inform bots not to index or follow those pages</li>
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<li>Also, I implemented an nginx rate limit of twelve requests per minute on all dynamic pages… I figure a human user might legitimately request one every five seconds</li>
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</ul>
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<h2 id="2018-11-05">2018-11-05</h2>
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<ul>
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<li>I wrote a small Python script <a href="https://gist.github.com/alanorth/4ff81d5f65613814a66cb6f84fdf1fc5">add-dc-rights.py</a> to add usage rights (<code>dc.rights</code>) to CGSpace items based on the CSV Hector gave me from MARLO:</li>
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</ul>
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<pre><code>$ ./add-dc-rights.py -i /tmp/marlo.csv -db dspace -u dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>The file <code>marlo.csv</code> was cleaned up and formatted in Open Refine</li>
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<li>165 of the items in their 2017 data are from CGSpace!</li>
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<li>I will add the data to CGSpace this week (done!)</li>
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<li>Jesus, is Facebook <em>trying</em> to be annoying?</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "05/Nov/2018" | grep -c "2a03:2880:11ff:"
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29889
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# grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a03:2880:11ff' dspace.log.2018-11-05 | sort | uniq
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29156
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# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "05/Nov/2018" | grep "2a03:2880:11ff:" | grep -c -E "(handle|bitstream)"
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29896
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</code></pre>
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<ul>
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<li>29,000 requests from Facebook, 29,000 Tomcat sessions, and none of the requests are to the dynamic pages I rate limited yesterday!</li>
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</ul>
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<h2 id="2018-11-06">2018-11-06</h2>
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<ul>
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<li>I updated all the <a href="https://github.com/ilri/DSpace/wiki/Scripts">DSpace helper Python scripts</a> to validate against PEP 8 using Flake8</li>
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<li>While I was updating the <a href="https://gist.github.com/alanorth/ddd7f555f0e487fe0e9d3eb4ff26ce50">rest-find-collections.py</a> script I noticed it was using <code>expand=all</code> to get the collection and community IDs</li>
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<li>I realized I actually only need <code>expand=collections,subCommunities</code>, and I wanted to see how much overhead the extra expands created so I did three runs of each:</li>
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</ul>
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<pre><code>$ time ./rest-find-collections.py 10568/27629 --rest-url https://dspacetest.cgiar.org/rest
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</code></pre>
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<ul>
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<li>Average time with all expands was 14.3 seconds, and 12.8 seconds with <code>collections,subCommunities</code>, so <strong>1.5 seconds difference</strong>!</li>
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</ul>
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<h2 id="2018-11-07">2018-11-07</h2>
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<ul>
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<li>Update my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to use a database management class with Python contexts so that connections and cursors are automatically opened and closed</li>
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<li>Tag version 0.7.0 of the dspace-statistics-api</li>
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</ul>
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<h2 id="2018-11-08">2018-11-08</h2>
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<ul>
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<li>I deployed verison 0.7.0 of the dspace-statistics-api on DSpace Test (linode19) so I can test it for a few days (and check the Munin stats to see the change in database connections) before deploying on CGSpace</li>
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|
<li>I also enabled systemd’s persistent journal by setting <a href="https://www.freedesktop.org/software/systemd/man/journald.conf.html"><code>Storage=persistent</code> in <em>journald.conf</em></a></li>
|
|
<li>Apparently <a href="https://www.freedesktop.org/software/systemd/man/journald.conf.html">Ubuntu 16.04 defaulted to using rsyslog for boot records until early 2018</a>, so I removed <code>rsyslog</code> too</li>
|
|
<li>Proof 277 IITA records on DSpace Test: <a href="https://dspacetest.cgiar.org/handle/10568/107871">IITA_ ALIZZY1802-csv_oct23</a>
|
|
|
|
<ul>
|
|
<li>There were a few issues with countries, a few language erorrs, a few whitespace errors, and then a handful of ISSNs in the ISBN field</li>
|
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</ul></li>
|
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</ul>
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<h2 id="2018-11-11">2018-11-11</h2>
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|
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<ul>
|
|
<li>I added tests to the <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a>!</li>
|
|
<li>It runs with Python 3.5, 3.6, and 3.7 using pytest, including automatically on Travis CI!</li>
|
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</ul>
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<h2 id="2018-11-13">2018-11-13</h2>
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|
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<ul>
|
|
<li>Help troubleshoot an issue with Judy Kimani submitting to the <em>ILRI project reports, papers and documents</em> collection on CGSpace</li>
|
|
<li>For some reason there is an existing group for the “Accept/Reject” workflow step, but it’s empty</li>
|
|
<li>I added Judy to the group and told her to try again</li>
|
|
<li>Sisay changed his leave to be full days until December so I need to finish the IITA records that he was working on (<a href="https://dspacetest.cgiar.org/handle/10568/107871">IITA_ ALIZZY1802-csv_oct23</a></li>
|
|
<li>Sisay had said there were a few PDFs missing and Bosede sent them this week, so I had to find those items on DSpace Test and add the bitstreams to the items manually</li>
|
|
<li>As for the collection mappings I think I need to export the CSV from DSpace Test, add mappings for each type (ie Books go to IITA books collection, etc), then re-import to DSpace Test, then export from DSpace command line in “migrate” mode…</li>
|
|
<li>From there I should be able to script the removal of the old DSpace Test collection so they just go to the correct IITA collections on import into CGSpace</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-11-14">2018-11-14</h2>
|
|
|
|
<ul>
|
|
<li>Finally import the 277 IITA (ALIZZY1802) records to CGSpace</li>
|
|
<li>I had to export them from DSpace Test and import them into a temporary collection on CGSpace first, then export the collection as CSV to map them to new owning collections (IITA books, IITA posters, etc) with OpenRefine because DSpace’s <code>dspace export</code> command doesn’t include the collections for the items!</li>
|
|
<li>Delete all old IITA collections on DSpace Test and run <code>dspace cleanup</code> to get rid of all the bitstreams</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-11-15">2018-11-15</h2>
|
|
|
|
<ul>
|
|
<li>Deploy version 0.8.1 of the <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to CGSpace (linode18)</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-11-18">2018-11-18</h2>
|
|
|
|
<ul>
|
|
<li>Request invoice from Wild Jordan for their meeting venue in January</li>
|
|
</ul>
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<!-- vim: set sw=2 ts=2: -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2018-11/">November, 2018</a></li>
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<li><a href="/cgspace-notes/2018-10/">October, 2018</a></li>
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<li><a href="/cgspace-notes/2018-09/">September, 2018</a></li>
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<li><a href="/cgspace-notes/2018-08/">August, 2018</a></li>
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<li><a href="/cgspace-notes/2018-07/">July, 2018</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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|
|
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
|
|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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<p>
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