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<meta property="og:description" content="2020-03-02
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Update dspace-statistics-api for DSpace 6+ UUIDs
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Tag version 1.2.0 on GitHub
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Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased SolrUpgradePre6xStatistics.java
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You need to download this into the DSpace 6.x source and compile it
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<meta name="twitter:title" content="March, 2020"/>
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<meta name="twitter:description" content="2020-03-02
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Update dspace-statistics-api for DSpace 6+ UUIDs
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Tag version 1.2.0 on GitHub
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Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased SolrUpgradePre6xStatistics.java
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You need to download this into the DSpace 6.x source and compile it
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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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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2020-03-02">2020-03-02</h2>
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<ul>
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<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
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<ul>
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<li>Tag version 1.2.0 on GitHub</li>
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</ul>
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</li>
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<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
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<ul>
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<li>You need to download this into the DSpace 6.x source and compile it</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
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$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x
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</code></pre><h2 id="2020-03-03">2020-03-03</h2>
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<ul>
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<li>Skype with Peter and Abenet to discuss the CG Core survey
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<ul>
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<li>We also discussed some other CGSpace issues</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-03-04">2020-03-04</h2>
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<ul>
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<li>Abenet asked me to add some new ILRI subjects to CGSpace
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<ul>
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<li>I <a href="https://github.com/ilri/DSpace/commit/b51a242e773bd8658d3cab4ac883975708b00386">updated the input-forms.xml</a> in our <code>5_x-prod</code> branch on GitHub</li>
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<li>Abenet said we are changing <code>HEALTH</code> to <code>HUMAN HEALTH</code> so I need to fix those using my <code>fix-metadata-values.py</code> script:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i 2020-03-04-fix-1-ilri-subject.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.ilri -m 203 -t correct -d
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</code></pre><ul>
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<li>But I have not run it on CGSpace yet because we want to ask Peter if he is sure about it…</li>
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<li>Send a message to Macaroni Bros to ask them about their Drupal module and its readiness for DSpace 6 UUIDs</li>
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</ul>
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<h2 id="2020-03-05">2020-03-05</h2>
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<ul>
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<li>I found a very <a href="https://lucene.apache.org/solr/guide/8_1/solr-system-requirements.html#lucene-solr-prior-to-7-0">interesting comment on the Solr 8.1 guide</a> about Java compatibility:</li>
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</ul>
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<blockquote>
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<p>Lucene/Solr 7.0 was the first version that successfully passed our tests using Java 9 and higher. You should avoid Java 9 or later for Lucene/Solr 6.x or earlier.</p>
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</blockquote>
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<h2 id="2020-03-08">2020-03-08</h2>
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<ul>
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<li>I want to try to consolidate our yearly Solr statistics cores back into one <code>statistics</code> core using the solr-import-export-json tool</li>
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<li>I will try it on DSpace test, doing one year at a time:</li>
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</ul>
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<pre><code>$ ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o /tmp/statistics-2010.json -k uid
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$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2010.json -k uid
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$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2010*</query></delete>"
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$ ./run.sh -s http://localhost:8081/solr/statistics-2011 -a export -o /tmp/statistics-2011.json -k uid
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$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2011.json -k uid
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$ curl -s "http://localhost:8081/solr/statistics-2011/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2011*</query></delete>"
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$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2012.json -k uid
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$ curl -s 'http://localhost:8081/solr/statistics/select?q=time:2012*&rows=0&wt=json&indent=true' | grep numFound
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"response":{"numFound":3761989,"start":0,"docs":[]
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$ curl -s 'http://localhost:8081/solr/statistics-2012/select?q=time:2012*&rows=0&wt=json&indent=true' | grep numFound
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"response":{"numFound":3761989,"start":0,"docs":[]
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$ curl -s "http://localhost:8081/solr/statistics-2012/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2012*</query></delete>"
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</code></pre><ul>
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<li>I will do this for as many cores as I can (disk space limited) and then monitor the effect on the system and JVM memory usage
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<ul>
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<li>Exporting half years might work, using a filter query with months as a regular expression:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ ./run.sh -s http://localhost:8081/solr/statistics-2014 -a export -o /tmp/statistics-2014-1.json -k uid -f 'time:/2014-0[1-6].*/'
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</code></pre><ul>
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<li>Upgrade PostgreSQL from 9.6 to 10 on DSpace Test (linode19)
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<ul>
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<li>I’ve been running it for one month in my local environment, and others have reported on the dspace-tech mailing list that they are using 10 and 11</li>
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</ul>
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</li>
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</ul>
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<pre><code># apt install postgresql-10 postgresql-contrib-10
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# systemctl stop tomcat7
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# pg_ctlcluster 9.6 main stop
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# tar -cvzpf var-lib-postgresql-9.6.tar.gz /var/lib/postgresql/9.6
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# tar -cvzpf etc-postgresql-9.6.tar.gz /etc/postgresql/9.6
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# pg_ctlcluster 10 main stop
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# pg_dropcluster 10 main
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# pg_upgradecluster 9.6 main
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# pg_dropcluster 9.6 main
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# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r
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</code></pre><h2 id="2020-03-09">2020-03-09</h2>
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<ul>
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<li>Peter noticed that the Solr stats were not showing anything before 2020
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<ul>
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<li>I had to restart Tomcat three times before all cores loaded properly…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-03-10">2020-03-10</h2>
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<ul>
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<li>Fix some logic issues in the nginx config
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<ul>
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<li>Use generic blocking of <code>[Bb]ot</code> and <code>[Cc]rawl</code> and <code>[Ss]pider</code> in the “badbots” rate limiting logic instead of trying to list them all one by one (bots should not be trying to index dynamic pages <em>no matter what</em> so we punish hard here)</li>
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<li>We were not properly forwarding the remote IP address to Tomcat in all nginx location blocks, which led some locations to log a hit from 127.0.0.1 (because we need to explicitly add the global proxy params when setting other headers in location blocks)</li>
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<li>Unfortunately this affected the REST API and there are a few hundred thousand requests from this user agent:</li>
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</ul>
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</li>
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</ul>
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<pre><code>Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 3.5.30729)
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</code></pre><ul>
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<li>It seems to only be a problem in the last week:</li>
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</ul>
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<pre><code># zgrep -c 64.225.40.66 /var/log/nginx/rest.log.{1..9}
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/var/log/nginx/rest.log.1:0
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/var/log/nginx/rest.log.2:0
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/var/log/nginx/rest.log.3:0
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/var/log/nginx/rest.log.4:3625
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/var/log/nginx/rest.log.5:27458
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/var/log/nginx/rest.log.6:0
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/var/log/nginx/rest.log.7:0
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/var/log/nginx/rest.log.8:0
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/var/log/nginx/rest.log.9:0
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</code></pre><ul>
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<li>In Solr the IP is 127.0.0.1, but in the nginx logs I can luckily see the real IP (64.225.40.66), which is on Digital Ocean</li>
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<li>I will purge them from Solr statistics:</li>
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</ul>
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<pre><code>$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>userAgent:"Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 3.5.30729)"</query></delete>'
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</code></pre><ul>
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<li>Another user agent that seems to be a bot is:</li>
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</ul>
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<pre><code>Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)
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</code></pre><ul>
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<li>In Solr the IP is 127.0.0.1 because of the misconfiguration, but in nginx’s logs I see it belongs to three IPs on Online.net in France:</li>
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</ul>
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<pre><code># zcat /var/log/nginx/access.log.*.gz /var/log/nginx/rest.log.*.gz | grep 'Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)' | awk '{print $1}' | sort | uniq -c
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63090 163.172.68.99
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183428 163.172.70.248
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147608 163.172.71.24
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</code></pre><ul>
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<li>It is making 10,000 to 40,000 requests to XMLUI per day…</li>
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</ul>
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<pre><code># zgrep -c 'Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)' /var/log/nginx/access.log.{1..9}
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/var/log/nginx/access.log.30.gz:18687
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/var/log/nginx/access.log.31.gz:28936
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/var/log/nginx/access.log.32.gz:36402
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/var/log/nginx/access.log.33.gz:38886
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/var/log/nginx/access.log.34.gz:30607
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/var/log/nginx/access.log.35.gz:19040
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/var/log/nginx/access.log.36.gz:10780
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/var/log/nginx/access.log.37.gz:5808
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/var/log/nginx/access.log.38.gz:3100
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/var/log/nginx/access.log.39.gz:1485
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/var/log/nginx/access.log.3.gz:2898
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/var/log/nginx/access.log.40.gz:373
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/var/log/nginx/access.log.41.gz:3909
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/var/log/nginx/access.log.42.gz:4729
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/var/log/nginx/access.log.43.gz:3906
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</code></pre><ul>
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<li>I will purge those hits too!</li>
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</ul>
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<pre><code>$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>userAgent:"Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)"</query></delete>'
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</code></pre><ul>
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<li>Shit, and something happened and a few thousand hits from user agents with “Bot” in their user agent got through
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<ul>
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<li>I need to re-run the <code>check-bot-hits.sh</code> script with the standard COUNTER-Robots list again, but add my own versions of a few because the script/Solr doesn’t support case-insensitive regular expressions:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ ./check-spider-hits.sh -f /tmp/bots -d -p
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(DEBUG) Using spiders pattern file: /tmp/bots
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(DEBUG) Checking for hits from spider: Citoid
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Purging 11 hits from Citoid in statistics
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(DEBUG) Checking for hits from spider: ecointernet
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Purging 375 hits from ecointernet in statistics
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(DEBUG) Checking for hits from spider: ^Pattern\/[0-9]
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Purging 1 hits from ^Pattern\/[0-9] in statistics
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(DEBUG) Checking for hits from spider: sqlmap
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(DEBUG) Checking for hits from spider: Typhoeus
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Purging 6 hits from Typhoeus in statistics
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(DEBUG) Checking for hits from spider: 7siters
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(DEBUG) Checking for hits from spider: Apache-HttpClient
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Purging 3178 hits from Apache-HttpClient in statistics
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Total number of bot hits purged: 3571
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$ ./check-spider-hits.sh -f /tmp/bots -d -p
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(DEBUG) Using spiders pattern file: /tmp/bots
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(DEBUG) Checking for hits from spider: [Bb]ot
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Purging 8317 hits from [Bb]ot in statistics
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(DEBUG) Checking for hits from spider: [Cc]rawl
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Purging 1314 hits from [Cc]rawl in statistics
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(DEBUG) Checking for hits from spider: [Ss]pider
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Purging 62 hits from [Ss]pider in statistics
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(DEBUG) Checking for hits from spider: Citoid
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(DEBUG) Checking for hits from spider: ecointernet
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(DEBUG) Checking for hits from spider: ^Pattern\/[0-9]
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(DEBUG) Checking for hits from spider: sqlmap
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(DEBUG) Checking for hits from spider: Typhoeus
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(DEBUG) Checking for hits from spider: 7siters
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(DEBUG) Checking for hits from spider: Apache-HttpClient
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</code></pre><!-- raw HTML omitted -->
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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/2020-03/">March, 2020</a></li>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
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<li><a href="/cgspace-notes/2019-12/">December, 2019</a></li>
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<li><a href="/cgspace-notes/2019-11/">November, 2019</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>
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<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 dir="auto">
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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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<p>
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<a href="#">Back to top</a>
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</p>
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</footer>
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</body>
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</html>
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