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href="https://alanorth.github.io/cgspace-notes/posts/index.xml" title="CGSpace Notes" /> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1> <p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2> <p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2020-06-01">2020-06-01</h2> <ul> <li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday <ul> <li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li> </ul> </li> <li>In other news, I checked the statistics API on DSpace 6 and it’s working</li> <li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2> <p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 02, 2020</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2020-05-02">2020-05-02</h2> <ul> <li>Peter said that CTA is having problems submitting an item to CGSpace <ul> <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> <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> </ul> </li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2020-05/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-04/">April, 2020</a></h2> <p class="blog-post-meta"><time datetime="2020-04-02T10:53:24+03:00">Thu Apr 02, 2020</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2020-04-02">2020-04-02</h2> <ul> <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 <ul> <li>I updated the fifty-eight existing items on CGSpace</li> </ul> </li> <li>Looking into the items Udana had asked about last week that were missing Altmetric donuts: <ul> <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> <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> <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> </ul> </li> <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> </ul> <a href='https://alanorth.github.io/cgspace-notes/2020-04/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2> <p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2020-03-02">2020-03-02</h2> <ul> <li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs <ul> <li>Tag version 1.2.0 on GitHub</li> </ul> </li> <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> <ul> <li>You need to download this into the DSpace 6.x source and compile it</li> </ul> </li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2> <p class="blog-post-meta"><time datetime="2020-02-02T11:56:30+02:00">Sun Feb 02, 2020</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2020-02-02">2020-02-02</h2> <ul> <li>Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday <ul> <li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li> <li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li> <li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li> <li>The code finally builds and runs with a fresh install</li> </ul> </li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2020-02/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-01/">January, 2020</a></h2> <p class="blog-post-meta"><time datetime="2020-01-06T10:48:30+02:00">Mon Jan 06, 2020</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2020-01-06">2020-01-06</h2> <ul> <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> <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 <ul> <li>The score is now linked to the DOI</li> <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> <li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li> </ul> </li> </ul> <h2 id="2020-01-07">2020-01-07</h2> <ul> <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 <ul> <li>The DOI has a score of 259, but the Handle has no score at all</li> <li>I <a href="https://twitter.com/mralanorth/status/1214471427157626881">tweeted</a> the CGSpace repository link</li> </ul> </li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2020-01/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-12/">December, 2019</a></h2> <p class="blog-post-meta"><time datetime="2019-12-01T11:22:30+02:00">Sun Dec 01, 2019</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2019-12-01">2019-12-01</h2> <ul> <li>Upgrade CGSpace (linode18) to Ubuntu 18.04: <ul> <li>Check any packages that have residual configs and purge them:</li> <li><!-- raw HTML omitted --># dpkg -l | grep -E ‘^rc’ | awk ‘{print $2}’ | xargs dpkg -P<!-- raw HTML omitted --></li> <li>Make sure all packages are up to date and the package manager is up to date, then reboot:</li> </ul> </li> </ul> <pre><code># apt update && apt full-upgrade # apt-get autoremove && apt-get autoclean # dpkg -C # reboot </code></pre> <a href='https://alanorth.github.io/cgspace-notes/2019-12/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-11/">November, 2019</a></h2> <p class="blog-post-meta"><time datetime="2019-11-04T12:20:30+02:00">Mon Nov 04, 2019</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2019-11-04">2019-11-04</h2> <ul> <li>Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics <ul> <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> </ul> </li> </ul> <pre><code># zcat --force /var/log/nginx/*access.log.*.gz | grep -cE "[0-9]{1,2}/Oct/2019" 4671942 # zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE "[0-9]{1,2}/Oct/2019" 1277694 </code></pre><ul> <li>So 4.6 million from XMLUI and another 1.2 million from API requests</li> <li>Let’s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):</li> </ul> <pre><code># zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E "[0-9]{1,2}/Oct/2019" 1183456 # zcat --force /var/log/nginx/rest.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E "/rest/bitstreams" 106781 </code></pre> <a href='https://alanorth.github.io/cgspace-notes/2019-11/'>Read more →</a> </article> <article class="blog-post"> <header> <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> <p class="blog-post-meta"><time datetime="2019-10-28T13:27:35+02:00">Mon Oct 28, 2019</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> <span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/migration/" rel="tag">Migration</a> </p> </header> <p>Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2.</p> <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> <a href='https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-10/">October, 2019</a></h2> <p class="blog-post-meta"><time datetime="2019-10-01T13:20:51+03:00">Tue Oct 01, 2019</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a> </p> </header> 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. <a href='https://alanorth.github.io/cgspace-notes/2019-10/'>Read more →</a> </article> <nav class="blog-pagination"> <a class="btn btn-outline-primary" href="/cgspace-notes/posts/" rel="prev" role="button">Previous page</a> <a class="btn btn-outline-primary" 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