Notes on CGSpace Notes https://alanorth.github.io/cgspace-notes/categories/notes/ Recent content in Notes on CGSpace Notes Hugo -- gohugo.io en-us Thu, 02 Jul 2020 15:35:54 +0300 August, 2020 https://alanorth.github.io/cgspace-notes/2020-07/ Thu, 02 Jul 2020 15:35:54 +0300 https://alanorth.github.io/cgspace-notes/2020-07/ <h2 id="2020-08-02">2020-08-02</h2> <ul> <li>I spent a few days working on a Java-based curation task to tag items with ISO 3166-1 Alpha2 country codes based on their <code>cg.coverage.country</code> text values <ul> <li>It looks up the names in ISO 3166-1 first, and then in our CGSpace countries mapping (which has five or so of Peter&rsquo;s preferred &ldquo;display&rdquo; country names)</li> <li>It implements a &ldquo;force&rdquo; mode too that will clear existing country codes and re-tag everything</li> <li>It is class based so I can easily add support for other vocabularies, and the technique could even be used for organizations with mappings to ROR and Clarisa&hellip;</li> </ul> </li> </ul> July, 2020 https://alanorth.github.io/cgspace-notes/2020-07/ Wed, 01 Jul 2020 10:53:54 +0300 https://alanorth.github.io/cgspace-notes/2020-07/ <h2 id="2020-07-01">2020-07-01</h2> <ul> <li>A few users noticed that CGSpace wasn&rsquo;t loading items today, item pages seem blank <ul> <li>I looked at the PostgreSQL locks but they don&rsquo;t seem unusual</li> <li>I guess this is the same &ldquo;blank item page&rdquo; issue that we had a few times in 2019 that we never solved</li> <li>I restarted Tomcat and PostgreSQL and the issue was gone</li> </ul> </li> <li>Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the <code>5_x-prod</code> branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter&rsquo;s request</li> </ul> June, 2020 https://alanorth.github.io/cgspace-notes/2020-06/ Mon, 01 Jun 2020 13:55:39 +0300 https://alanorth.github.io/cgspace-notes/2020-06/ <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&rsquo;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> May, 2020 https://alanorth.github.io/cgspace-notes/2020-05/ Sat, 02 May 2020 09:52:04 +0300 https://alanorth.github.io/cgspace-notes/2020-05/ <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 &lsquo;idle in transaction&rsquo; and &lsquo;waiting for lock&rsquo; 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> April, 2020 https://alanorth.github.io/cgspace-notes/2020-04/ Thu, 02 Apr 2020 10:53:24 +0300 https://alanorth.github.io/cgspace-notes/2020-04/ <h2 id="2020-04-02">2020-04-02</h2> <ul> <li>Maria asked me to update Charles Staver&rsquo;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> March, 2020 https://alanorth.github.io/cgspace-notes/2020-03/ Mon, 02 Mar 2020 12:31:30 +0200 https://alanorth.github.io/cgspace-notes/2020-03/ <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> February, 2020 https://alanorth.github.io/cgspace-notes/2020-02/ Sun, 02 Feb 2020 11:56:30 +0200 https://alanorth.github.io/cgspace-notes/2020-02/ <h2 id="2020-02-02">2020-02-02</h2> <ul> <li>Continue working on porting CGSpace&rsquo;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> January, 2020 https://alanorth.github.io/cgspace-notes/2020-01/ Mon, 06 Jan 2020 10:48:30 +0200 https://alanorth.github.io/cgspace-notes/2020-01/ <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> December, 2019 https://alanorth.github.io/cgspace-notes/2019-12/ Sun, 01 Dec 2019 11:22:30 +0200 https://alanorth.github.io/cgspace-notes/2019-12/ <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 &lsquo;^rc&rsquo; | awk &lsquo;{print $2}&rsquo; | 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 &amp;&amp; apt full-upgrade # apt-get autoremove &amp;&amp; apt-get autoclean # dpkg -C # reboot </code></pre> November, 2019 https://alanorth.github.io/cgspace-notes/2019-11/ Mon, 04 Nov 2019 12:20:30 +0200 https://alanorth.github.io/cgspace-notes/2019-11/ <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 &quot;[0-9]{1,2}/Oct/2019&quot; 4671942 # zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE &quot;[0-9]{1,2}/Oct/2019&quot; 1277694 </code></pre><ul> <li>So 4.6 million from XMLUI and another 1.2 million from API requests</li> <li>Let&rsquo;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 &quot;[0-9]{1,2}/Oct/2019&quot; 1183456 # zcat --force /var/log/nginx/rest.log.*.gz | grep -E &quot;[0-9]{1,2}/Oct/2019&quot; | grep -c -E &quot;/rest/bitstreams&quot; 106781 </code></pre> CGSpace CG Core v2 Migration https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/ Mon, 28 Oct 2019 13:27:35 +0200 https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/ <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> October, 2019 https://alanorth.github.io/cgspace-notes/2019-10/ Tue, 01 Oct 2019 13:20:51 +0300 https://alanorth.github.io/cgspace-notes/2019-10/ 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&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c 'id,dc. September, 2019 https://alanorth.github.io/cgspace-notes/2019-09/ Sun, 01 Sep 2019 10:17:51 +0300 https://alanorth.github.io/cgspace-notes/2019-09/ <h2 id="2019-09-01">2019-09-01</h2> <ul> <li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li> <li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li> </ul> <pre><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 440 17.58.101.255 441 157.55.39.101 485 207.46.13.43 728 169.60.128.125 730 207.46.13.108 758 157.55.39.9 808 66.160.140.179 814 207.46.13.212 2472 163.172.71.23 6092 3.94.211.189 # 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 &quot;01/Sep/2019:0&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 33 2a01:7e00::f03c:91ff:fe16:fcb 57 3.83.192.124 57 3.87.77.25 57 54.82.1.8 822 2a01:9cc0:47:1:1a:4:0:2 1223 45.5.184.72 1633 172.104.229.92 5112 205.186.128.185 7249 2a01:7e00::f03c:91ff:fe18:7396 9124 45.5.186.2 </code></pre> August, 2019 https://alanorth.github.io/cgspace-notes/2019-08/ Sat, 03 Aug 2019 12:39:51 +0300 https://alanorth.github.io/cgspace-notes/2019-08/ <h2 id="2019-08-03">2019-08-03</h2> <ul> <li>Look at Bioversity&rsquo;s latest migration CSV and now I see that Francesco has cleaned up the extra columns and the newline at the end of the file, but many of the column headers have an extra space in the name&hellip;</li> </ul> <h2 id="2019-08-04">2019-08-04</h2> <ul> <li>Deploy ORCID identifier updates requested by Bioversity to CGSpace</li> <li>Run system updates on CGSpace (linode18) and reboot it <ul> <li>Before updating it I checked Solr and verified that all statistics cores were loaded properly&hellip;</li> <li>After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s lucky.</li> </ul> </li> <li>Run system updates on DSpace Test (linode19) and reboot it</li> </ul> July, 2019 https://alanorth.github.io/cgspace-notes/2019-07/ Mon, 01 Jul 2019 12:13:51 +0300 https://alanorth.github.io/cgspace-notes/2019-07/ <h2 id="2019-07-01">2019-07-01</h2> <ul> <li>Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice</li> <li>Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace: <ul> <li><a href="https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">DSpace Test</a></li> <li><a href="https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">CGSpace</a></li> </ul> </li> <li>Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community</li> </ul> June, 2019 https://alanorth.github.io/cgspace-notes/2019-06/ Sun, 02 Jun 2019 10:57:51 +0300 https://alanorth.github.io/cgspace-notes/2019-06/ <h2 id="2019-06-02">2019-06-02</h2> <ul> <li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li> <li>Run system updates on CGSpace (linode18) and reboot it</li> </ul> <h2 id="2019-06-03">2019-06-03</h2> <ul> <li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li> </ul> May, 2019 https://alanorth.github.io/cgspace-notes/2019-05/ Wed, 01 May 2019 07:37:43 +0300 https://alanorth.github.io/cgspace-notes/2019-05/ <h2 id="2019-05-01">2019-05-01</h2> <ul> <li>Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace</li> <li>A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items <ul> <li>Apparently if the item is in the <code>workflowitem</code> table it is submitted to a workflow</li> <li>And if it is in the <code>workspaceitem</code> table it is in the pre-submitted state</li> </ul> </li> <li>The item seems to be in a pre-submitted state, so I tried to delete it from there:</li> </ul> <pre><code>dspace=# DELETE FROM workspaceitem WHERE item_id=74648; DELETE 1 </code></pre><ul> <li>But after this I tried to delete the item from the XMLUI and it is <em>still</em> present&hellip;</li> </ul> April, 2019 https://alanorth.github.io/cgspace-notes/2019-04/ Mon, 01 Apr 2019 09:00:43 +0300 https://alanorth.github.io/cgspace-notes/2019-04/ <h2 id="2019-04-01">2019-04-01</h2> <ul> <li>Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc <ul> <li>They asked if we had plans to enable RDF support in CGSpace</li> </ul> </li> <li>There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today <ul> <li>I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!</li> </ul> </li> </ul> <pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep 'Spore-192-EN-web.pdf' | grep -E '(18.196.196.108|18.195.78.144|18.195.218.6)' | awk '{print $9}' | sort | uniq -c | sort -n | tail -n 5 4432 200 </code></pre><ul> <li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li> <li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li> </ul> <pre><code>$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.country -m 228 -t ACTION -d $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -m 231 -t action -d $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d </code></pre> March, 2019 https://alanorth.github.io/cgspace-notes/2019-03/ Fri, 01 Mar 2019 12:16:30 +0100 https://alanorth.github.io/cgspace-notes/2019-03/ <h2 id="2019-03-01">2019-03-01</h2> <ul> <li>I checked IITA&rsquo;s 259 Feb 14 records from last month for duplicates using Atmire&rsquo;s Duplicate Checker on a fresh snapshot of CGSpace on my local machine and everything looks good</li> <li>I am now only waiting to hear from her about where the items should go, though I assume Journal Articles go to IITA Journal Articles collection, etc&hellip;</li> <li>Looking at the other half of Udana&rsquo;s WLE records from 2018-11 <ul> <li>I finished the ones for Restoring Degraded Landscapes (RDL), but these are for Variability, Risks and Competing Uses (VRC)</li> <li>I did the usual cleanups for whitespace, added regions where they made sense for certain countries, cleaned up the DOI link formats, added rights information based on the publications page for a few items</li> <li>Most worryingly, there are encoding errors in the abstracts for eleven items, for example:</li> <li>68.15% � 9.45 instead of 68.15% ± 9.45</li> <li>2003�2013 instead of 2003–2013</li> </ul> </li> <li>I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs</li> </ul> February, 2019 https://alanorth.github.io/cgspace-notes/2019-02/ Fri, 01 Feb 2019 21:37:30 +0200 https://alanorth.github.io/cgspace-notes/2019-02/ <h2 id="2019-02-01">2019-02-01</h2> <ul> <li>Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!</li> <li>The top IPs before, during, and after this latest alert tonight were:</li> </ul> <pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;01/Feb/2019:(17|18|19|20|21)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 245 207.46.13.5 332 54.70.40.11 385 5.143.231.38 405 207.46.13.173 405 207.46.13.75 1117 66.249.66.219 1121 35.237.175.180 1546 5.9.6.51 2474 45.5.186.2 5490 85.25.237.71 </code></pre><ul> <li><code>85.25.237.71</code> is the &ldquo;Linguee Bot&rdquo; that I first saw last month</li> <li>The Solr statistics the past few months have been very high and I was wondering if the web server logs also showed an increase</li> <li>There were just over 3 million accesses in the nginx logs last month:</li> </ul> <pre><code># time zcat --force /var/log/nginx/* | grep -cE &quot;[0-9]{1,2}/Jan/2019&quot; 3018243 real 0m19.873s user 0m22.203s sys 0m1.979s </code></pre> January, 2019 https://alanorth.github.io/cgspace-notes/2019-01/ Wed, 02 Jan 2019 09:48:30 +0200 https://alanorth.github.io/cgspace-notes/2019-01/ <h2 id="2019-01-02">2019-01-02</h2> <ul> <li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li> <li>I don&rsquo;t see anything interesting in the web server logs around that time though:</li> </ul> <pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 92 40.77.167.4 99 210.7.29.100 120 38.126.157.45 177 35.237.175.180 177 40.77.167.32 216 66.249.75.219 225 18.203.76.93 261 46.101.86.248 357 207.46.13.1 903 54.70.40.11 </code></pre> December, 2018 https://alanorth.github.io/cgspace-notes/2018-12/ Sun, 02 Dec 2018 02:09:30 +0200 https://alanorth.github.io/cgspace-notes/2018-12/ <h2 id="2018-12-01">2018-12-01</h2> <ul> <li>Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK</li> <li>I manually installed OpenJDK, then removed Oracle JDK, then re-ran the <a href="http://github.com/ilri/rmg-ansible-public">Ansible playbook</a> to update all configuration files, etc</li> <li>Then I ran all system updates and restarted the server</li> </ul> <h2 id="2018-12-02">2018-12-02</h2> <ul> <li>I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another <a href="https://usn.ubuntu.com/3831-1/">Ghostscript vulnerability last week</a></li> </ul> November, 2018 https://alanorth.github.io/cgspace-notes/2018-11/ Thu, 01 Nov 2018 16:41:30 +0200 https://alanorth.github.io/cgspace-notes/2018-11/ <h2 id="2018-11-01">2018-11-01</h2> <ul> <li>Finalize AReS Phase I and Phase II ToRs</li> <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> </ul> <h2 id="2018-11-03">2018-11-03</h2> <ul> <li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li> <li>Today these are the top 10 IPs:</li> </ul> October, 2018 https://alanorth.github.io/cgspace-notes/2018-10/ Mon, 01 Oct 2018 22:31:54 +0300 https://alanorth.github.io/cgspace-notes/2018-10/ <h2 id="2018-10-01">2018-10-01</h2> <ul> <li>Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items</li> <li>I created a GitHub issue to track this <a href="https://github.com/ilri/DSpace/issues/389">#389</a>, because I&rsquo;m super busy in Nairobi right now</li> </ul> September, 2018 https://alanorth.github.io/cgspace-notes/2018-09/ Sun, 02 Sep 2018 09:55:54 +0300 https://alanorth.github.io/cgspace-notes/2018-09/ <h2 id="2018-09-02">2018-09-02</h2> <ul> <li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li> <li>I&rsquo;ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li> <li>Also, I&rsquo;ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month</li> <li>I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:</li> </ul> August, 2018 https://alanorth.github.io/cgspace-notes/2018-08/ Wed, 01 Aug 2018 11:52:54 +0300 https://alanorth.github.io/cgspace-notes/2018-08/ <h2 id="2018-08-01">2018-08-01</h2> <ul> <li>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</li> </ul> <pre><code>[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child [Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB [Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB </code></pre><ul> <li>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</li> <li>From the DSpace log I see that eventually Solr stopped responding, so I guess the <code>java</code> process that was OOM killed above was Tomcat&rsquo;s</li> <li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</li> <li>Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core</li> <li>The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes</li> <li>I ran all system updates on DSpace Test and rebooted it</li> </ul> July, 2018 https://alanorth.github.io/cgspace-notes/2018-07/ Sun, 01 Jul 2018 12:56:54 +0300 https://alanorth.github.io/cgspace-notes/2018-07/ <h2 id="2018-07-01">2018-07-01</h2> <ul> <li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li> </ul> <pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace </code></pre><ul> <li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li> </ul> <pre><code>There is insufficient memory for the Java Runtime Environment to continue. </code></pre> June, 2018 https://alanorth.github.io/cgspace-notes/2018-06/ Mon, 04 Jun 2018 19:49:54 -0700 https://alanorth.github.io/cgspace-notes/2018-06/ <h2 id="2018-06-04">2018-06-04</h2> <ul> <li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>) <ul> <li>There seems to be a problem with the CUA and L&amp;R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn&rsquo;t build</li> </ul> </li> <li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li> <li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li> </ul> <pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n </code></pre><ul> <li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="https://alanorth.github.io/cgspace-notes/cgspace-notes/2018-03/">March, 2018</a></li> <li>Time to index ~70,000 items on CGSpace:</li> </ul> <pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b real 74m42.646s user 8m5.056s sys 2m7.289s </code></pre> May, 2018 https://alanorth.github.io/cgspace-notes/2018-05/ Tue, 01 May 2018 16:43:54 +0300 https://alanorth.github.io/cgspace-notes/2018-05/ <h2 id="2018-05-01">2018-05-01</h2> <ul> <li>I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface: <ul> <li>http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E</li> <li>http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E</li> </ul> </li> <li>Then I reduced the JVM heap size from 6144 back to 5120m</li> <li>Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to support hosts choosing which distribution they want to use</li> </ul> April, 2018 https://alanorth.github.io/cgspace-notes/2018-04/ Sun, 01 Apr 2018 16:13:54 +0200 https://alanorth.github.io/cgspace-notes/2018-04/ <h2 id="2018-04-01">2018-04-01</h2> <ul> <li>I tried to test something on DSpace Test but noticed that it&rsquo;s down since god knows when</li> <li>Catalina logs at least show some memory errors yesterday:</li> </ul> March, 2018 https://alanorth.github.io/cgspace-notes/2018-03/ Fri, 02 Mar 2018 16:07:54 +0200 https://alanorth.github.io/cgspace-notes/2018-03/ <h2 id="2018-03-02">2018-03-02</h2> <ul> <li>Export a CSV of the IITA community metadata for Martin Mueller</li> </ul> February, 2018 https://alanorth.github.io/cgspace-notes/2018-02/ Thu, 01 Feb 2018 16:28:54 +0200 https://alanorth.github.io/cgspace-notes/2018-02/ <h2 id="2018-02-01">2018-02-01</h2> <ul> <li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li> <li>We don&rsquo;t need to distinguish between internal and external works, so that makes it just a simple list</li> <li>Yesterday I figured out how to monitor DSpace sessions using JMX</li> <li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu&rsquo;s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="https://alanorth.github.io/cgspace-notes/cgspace-notes/2018-01/">in 2018-01</a></li> </ul> January, 2018 https://alanorth.github.io/cgspace-notes/2018-01/ Tue, 02 Jan 2018 08:35:54 -0800 https://alanorth.github.io/cgspace-notes/2018-01/ <h2 id="2018-01-02">2018-01-02</h2> <ul> <li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li> <li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li> <li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li> <li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li> <li>And just before that I see this:</li> </ul> <pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000]. </code></pre><ul> <li>Ah hah! So the pool was actually empty!</li> <li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li> <li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li> <li>I notice this error quite a few times in dspace.log:</li> </ul> <pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32. </code></pre><ul> <li>And there are many of these errors every day for the past month:</li> </ul> <pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.* dspace.log.2017-11-21:4 dspace.log.2017-11-22:1 dspace.log.2017-11-23:4 dspace.log.2017-11-24:11 dspace.log.2017-11-25:0 dspace.log.2017-11-26:1 dspace.log.2017-11-27:7 dspace.log.2017-11-28:21 dspace.log.2017-11-29:31 dspace.log.2017-11-30:15 dspace.log.2017-12-01:15 dspace.log.2017-12-02:20 dspace.log.2017-12-03:38 dspace.log.2017-12-04:65 dspace.log.2017-12-05:43 dspace.log.2017-12-06:72 dspace.log.2017-12-07:27 dspace.log.2017-12-08:15 dspace.log.2017-12-09:29 dspace.log.2017-12-10:35 dspace.log.2017-12-11:20 dspace.log.2017-12-12:44 dspace.log.2017-12-13:36 dspace.log.2017-12-14:59 dspace.log.2017-12-15:104 dspace.log.2017-12-16:53 dspace.log.2017-12-17:66 dspace.log.2017-12-18:83 dspace.log.2017-12-19:101 dspace.log.2017-12-20:74 dspace.log.2017-12-21:55 dspace.log.2017-12-22:66 dspace.log.2017-12-23:50 dspace.log.2017-12-24:85 dspace.log.2017-12-25:62 dspace.log.2017-12-26:49 dspace.log.2017-12-27:30 dspace.log.2017-12-28:54 dspace.log.2017-12-29:68 dspace.log.2017-12-30:89 dspace.log.2017-12-31:53 dspace.log.2018-01-01:45 dspace.log.2018-01-02:34 </code></pre><ul> <li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains</li> </ul> December, 2017 https://alanorth.github.io/cgspace-notes/2017-12/ Fri, 01 Dec 2017 13:53:54 +0300 https://alanorth.github.io/cgspace-notes/2017-12/ <h2 id="2017-12-01">2017-12-01</h2> <ul> <li>Uptime Robot noticed that CGSpace went down</li> <li>The logs say &ldquo;Timeout waiting for idle object&rdquo;</li> <li>PostgreSQL activity says there are 115 connections currently</li> <li>The list of connections to XMLUI and REST API for today:</li> </ul> November, 2017 https://alanorth.github.io/cgspace-notes/2017-11/ Thu, 02 Nov 2017 09:37:54 +0200 https://alanorth.github.io/cgspace-notes/2017-11/ <h2 id="2017-11-01">2017-11-01</h2> <ul> <li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li> </ul> <h2 id="2017-11-02">2017-11-02</h2> <ul> <li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li> </ul> <pre><code># grep -c &quot;CORE&quot; /var/log/nginx/access.log 0 </code></pre><ul> <li>Generate list of authors on CGSpace for Peter to go through and correct:</li> </ul> <pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv; COPY 54701 </code></pre> October, 2017 https://alanorth.github.io/cgspace-notes/2017-10/ Sun, 01 Oct 2017 08:07:54 +0300 https://alanorth.github.io/cgspace-notes/2017-10/ <h2 id="2017-10-01">2017-10-01</h2> <ul> <li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li> </ul> <pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336 </code></pre><ul> <li>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li> <li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li> </ul> CGIAR Library Migration https://alanorth.github.io/cgspace-notes/cgiar-library-migration/ Mon, 18 Sep 2017 16:38:35 +0300 https://alanorth.github.io/cgspace-notes/cgiar-library-migration/ <p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p>