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481 lines
17 KiB
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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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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 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="2020-05-02">2020-05-02</h2>
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<ul>
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<li>Peter said that CTA is having problems submitting an item to CGSpace
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<ul>
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<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in ‘idle in transaction’ and ‘waiting for lock’ state are increasing again</li>
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<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-05/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-04/">April, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-04-02T10:53:24+03:00">Thu Apr 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="2020-04-02">2020-04-02</h2>
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<ul>
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<li>Maria asked me to update Charles Staver’s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
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<ul>
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<li>I updated the fifty-eight existing items on CGSpace</li>
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</ul>
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</li>
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<li>Looking into the items Udana had asked about last week that were missing Altmetric donuts:
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<ul>
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<li><a href="https://hdl.handle.net/10568/103225">The first</a> is still missing its DOI, so I added it and <a href="https://twitter.com/mralanorth/status/1245632619661766657">tweeted its handle</a> (after a few hours there was a donut with score 222)</li>
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<li><a href="https://hdl.handle.net/10568/106899">The second item</a> now has a donut with score 2 since I <a href="https://twitter.com/mralanorth/status/1243158045540134913">tweeted its handle</a> last week</li>
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<li><a href="https://hdl.handle.net/10568/107258">The third item</a> now has a donut with score 1 since I <a href="https://twitter.com/mralanorth/status/1243158786392625153">tweeted it</a> last week</li>
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</ul>
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</li>
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<li>On the same note, the <a href="https://hdl.handle.net/10568/106573">one item</a> Abenet pointed out last week now has a donut with score of 104 after I <a href="https://twitter.com/mralanorth/status/1243163710241345536">tweeted it</a> last week</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-04/'>Read more →</a>
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</article>
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<article class="blog-post">
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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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<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-02-02T11:56:30+02:00">Sun Feb 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="2020-02-02">2020-02-02</h2>
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<ul>
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<li>Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday
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<ul>
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<li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li>
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<li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li>
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<li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li>
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<li>The code finally builds and runs with a fresh install</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-02/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-01/">January, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-01-06T10:48:30+02:00">Mon Jan 06, 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="2020-01-06">2020-01-06</h2>
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<ul>
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<li>Open <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706">a ticket</a> with Atmire to request a quote for the upgrade to DSpace 6</li>
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<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
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<ul>
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<li>The score is now linked to the DOI</li>
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<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
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<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-01-07">2020-01-07</h2>
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<ul>
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<li>Peter Ballantyne highlighted one more WLE <a href="https://hdl.handle.net/10568/101286">item</a> that is missing the Altmetric score that its DOI has
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<ul>
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<li>The DOI has a score of 259, but the Handle has no score at all</li>
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<li>I <a href="https://twitter.com/mralanorth/status/1214471427157626881">tweeted</a> the CGSpace repository link</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-01/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-12/">December, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-12-01T11:22:30+02:00">Sun Dec 01, 2019</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="2019-12-01">2019-12-01</h2>
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<ul>
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<li>Upgrade CGSpace (linode18) to Ubuntu 18.04:
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<ul>
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<li>Check any packages that have residual configs and purge them:</li>
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<li><!-- raw HTML omitted --># dpkg -l | grep -E ‘^rc’ | awk ‘{print $2}’ | xargs dpkg -P<!-- raw HTML omitted --></li>
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<li>Make sure all packages are up to date and the package manager is up to date, then reboot:</li>
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</ul>
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</li>
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</ul>
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<pre><code># apt update && apt full-upgrade
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# apt-get autoremove && apt-get autoclean
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# dpkg -C
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# reboot
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2019-12/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-11/">November, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-11-04T12:20:30+02:00">Mon Nov 04, 2019</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="2019-11-04">2019-11-04</h2>
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<ul>
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<li>Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics
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<ul>
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<li>I looked in the nginx logs and see 4.6 million in the access logs, and 1.2 million in the API logs:</li>
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</ul>
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</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*access.log.*.gz | grep -cE "[0-9]{1,2}/Oct/2019"
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4671942
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# zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE "[0-9]{1,2}/Oct/2019"
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1277694
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</code></pre><ul>
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<li>So 4.6 million from XMLUI and another 1.2 million from API requests</li>
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<li>Let’s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E "[0-9]{1,2}/Oct/2019"
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1183456
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# zcat --force /var/log/nginx/rest.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E "/rest/bitstreams"
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106781
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2019-11/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></h2>
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<p class="blog-post-meta"><time datetime="2019-10-28T13:27:35+02:00">Mon Oct 28, 2019</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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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/migration/" rel="tag">Migration</a>
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</p>
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</header>
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<p>Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2.</p>
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<p>With reference to <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2 draft standard</a> by Marie-Angélique as well as <a href="http://www.dublincore.org/specifications/dublin-core/dcmi-terms/">DCMI DCTERMS</a>.</p>
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<a href='https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-10/">October, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-10-01T13:20:51+03:00">Tue Oct 01, 2019</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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2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U+00A0) there that would otherwise be removed by the csv-metadata-quality script’s “unneccesary Unicode” fix: $ csvcut -c 'id,dc.
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<a href='https://alanorth.github.io/cgspace-notes/2019-10/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-09/">September, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-09-01T10:17:51+03:00">Sun Sep 01, 2019</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="2019-09-01">2019-09-01</h2>
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<ul>
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<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
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<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E "01/Sep/2019:0" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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440 17.58.101.255
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441 157.55.39.101
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485 207.46.13.43
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728 169.60.128.125
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730 207.46.13.108
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758 157.55.39.9
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808 66.160.140.179
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814 207.46.13.212
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2472 163.172.71.23
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6092 3.94.211.189
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# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "01/Sep/2019:0" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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33 2a01:7e00::f03c:91ff:fe16:fcb
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57 3.83.192.124
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57 3.87.77.25
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57 54.82.1.8
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822 2a01:9cc0:47:1:1a:4:0:2
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1223 45.5.184.72
|
|
1633 172.104.229.92
|
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5112 205.186.128.185
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7249 2a01:7e00::f03c:91ff:fe18:7396
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9124 45.5.186.2
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|
</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2019-09/'>Read more →</a>
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