1089 lines
60 KiB
XML
1089 lines
60 KiB
XML
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||
<channel>
|
||
<title>Notes on CGSpace Notes</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/categories/notes/</link>
|
||
<description>Recent content in Notes on CGSpace Notes</description>
|
||
<generator>Hugo -- gohugo.io</generator>
|
||
<language>en-us</language>
|
||
<lastBuildDate>Wed, 01 Sep 2021 09:14:07 +0300</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" />
|
||
<item>
|
||
<title>September, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-09/</link>
|
||
<pubDate>Wed, 01 Sep 2021 09:14:07 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-09/</guid>
|
||
<description><h2 id="2021-09-02">2021-09-02</h2>
|
||
<ul>
|
||
<li>Troubleshooting the missing Altmetric scores on AReS
|
||
<ul>
|
||
<li>Turns out that I didn&rsquo;t actually fix them last month because the check for <code>content.altmetric</code> still exists, and I can&rsquo;t access the DOIs using <code>_h.source.DOI</code> for some reason</li>
|
||
<li>I can access all other kinds of item metadata using the Elasticsearch label, but not DOI!!!</li>
|
||
<li>I will change <code>DOI</code> to <code>tomato</code> in the repository setup and start a re-harvest&hellip; I need to see if this is some kind of reserved word or something&hellip;</li>
|
||
<li>Even as <code>tomato</code> I can&rsquo;t access that field as <code>_h.source.tomato</code> in Angular, but it does work as a filter source&hellip; sigh</li>
|
||
</ul>
|
||
</li>
|
||
<li>I&rsquo;m having problems using the OpenRXV API
|
||
<ul>
|
||
<li>The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search query properly&hellip;</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>August, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-08/</link>
|
||
<pubDate>Sun, 01 Aug 2021 09:01:07 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-08/</guid>
|
||
<description><h2 id="2021-08-01">2021-08-01</h2>
|
||
<ul>
|
||
<li>Update Docker images on AReS server (linode20) and reboot the server:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console"># docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
|
||
</code></pre><ul>
|
||
<li>I decided to upgrade linode20 from Ubuntu 18.04 to 20.04</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>July, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-07/</link>
|
||
<pubDate>Thu, 01 Jul 2021 08:53:07 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-07/</guid>
|
||
<description><h2 id="2021-07-01">2021-07-01</h2>
|
||
<ul>
|
||
<li>Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVOC for Enrico:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242, 187) GROUP BY subject ORDER BY count DESC) to /tmp/2021-07-01-all-subjects.csv WITH CSV HEADER;
|
||
COPY 20994
|
||
</code></pre></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>June, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-06/</link>
|
||
<pubDate>Tue, 01 Jun 2021 10:51:07 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-06/</guid>
|
||
<description><h2 id="2021-06-01">2021-06-01</h2>
|
||
<ul>
|
||
<li>IWMI notified me that AReS was down with an HTTP 502 error
|
||
<ul>
|
||
<li>Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification</li>
|
||
<li>I don&rsquo;t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the <code>angular_nginx</code> container isn&rsquo;t running</li>
|
||
<li>I simply started it and AReS was running again:</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>May, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-05/</link>
|
||
<pubDate>Sun, 02 May 2021 09:50:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-05/</guid>
|
||
<description><h2 id="2021-05-01">2021-05-01</h2>
|
||
<ul>
|
||
<li>I looked at the top user agents and IPs in the Solr statistics for last month and I see these user agents:
|
||
<ul>
|
||
<li>&ldquo;RI/1.0&rdquo;, 1337</li>
|
||
<li>&ldquo;Microsoft Office Word 2014&rdquo;, 941</li>
|
||
</ul>
|
||
</li>
|
||
<li>I will add the RI/1.0 pattern to our DSpace agents overload and purge them from Solr (we had previously seen this agent with 9,000 hits or so in 2020-09), but I think I will leave the Microsoft Word one&hellip; as that&rsquo;s an actual user&hellip;</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>April, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-04/</link>
|
||
<pubDate>Thu, 01 Apr 2021 09:50:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-04/</guid>
|
||
<description><h2 id="2021-04-01">2021-04-01</h2>
|
||
<ul>
|
||
<li>I wrote a script to query Sherpa&rsquo;s API for our ISSNs: <code>sherpa-issn-lookup.py</code>
|
||
<ul>
|
||
<li>I&rsquo;m curious to see how the results compare with the results from Crossref yesterday</li>
|
||
</ul>
|
||
</li>
|
||
<li>AReS Explorer was down since this morning, I didn&rsquo;t see anything in the systemd journal
|
||
<ul>
|
||
<li>I simply took everything down with docker-compose and then back up, and then it was OK</li>
|
||
<li>Perhaps one of the containers crashed, I should have looked closer but I was in a hurry</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>March, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-03/</link>
|
||
<pubDate>Mon, 01 Mar 2021 10:13:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-03/</guid>
|
||
<description><h2 id="2021-03-01">2021-03-01</h2>
|
||
<ul>
|
||
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
|
||
<ul>
|
||
<li>He&rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
|
||
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>CGSpace CG Core v2 Migration</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/</link>
|
||
<pubDate>Sun, 21 Feb 2021 13:27:35 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/</guid>
|
||
<description><p>Changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2. Implemented on 2021-02-21.</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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>February, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-02/</link>
|
||
<pubDate>Mon, 01 Feb 2021 10:13:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-02/</guid>
|
||
<description><h2 id="2021-02-01">2021-02-01</h2>
|
||
<ul>
|
||
<li>Abenet said that CIP found more duplicate records in their export from AReS
|
||
<ul>
|
||
<li>I re-opened <a href="https://github.com/ilri/OpenRXV/issues/67">the issue</a> on OpenRXV where we had previously noticed this</li>
|
||
<li>The shared link where the duplicates are is here: <a href="https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6">https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
|
||
<li>Check the results of the AReS harvesting from last night:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty'
|
||
{
|
||
&quot;count&quot; : 100875,
|
||
&quot;_shards&quot; : {
|
||
&quot;total&quot; : 1,
|
||
&quot;successful&quot; : 1,
|
||
&quot;skipped&quot; : 0,
|
||
&quot;failed&quot; : 0
|
||
}
|
||
}
|
||
</code></pre></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>January, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-01/</link>
|
||
<pubDate>Sun, 03 Jan 2021 10:13:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-01/</guid>
|
||
<description><h2 id="2021-01-03">2021-01-03</h2>
|
||
<ul>
|
||
<li>Peter notified me that some filters on AReS were broken again
|
||
<ul>
|
||
<li>It&rsquo;s the same issue with the field names getting <code>.keyword</code> appended to the end that I already <a href="https://github.com/ilri/OpenRXV/issues/66">filed an issue on OpenRXV about last month</a></li>
|
||
<li>I fixed the broken filters (careful to not edit any others, lest they break too!)</li>
|
||
</ul>
|
||
</li>
|
||
<li>Fix an issue with start page number for the DSpace REST API and statistics API in OpenRXV
|
||
<ul>
|
||
<li>The start page had been &ldquo;1&rdquo; in the UI, but in the backend they were doing some gymnastics to adjust to the zero-based offset/limit/page of the DSpace REST API and the statistics API</li>
|
||
<li>I adjusted it to default to 0 and added a note to the admin screen</li>
|
||
<li>I realized that this issue was actually causing the first page of 100 statistics to be missing&hellip;</li>
|
||
<li>For example, <a href="https://cgspace.cgiar.org/handle/10568/66839">this item</a> has 51 views on CGSpace, but 0 on AReS</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>December, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-12/</link>
|
||
<pubDate>Tue, 01 Dec 2020 11:32:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-12/</guid>
|
||
<description><h2 id="2020-12-01">2020-12-01</h2>
|
||
<ul>
|
||
<li>Atmire responded about the issue with duplicate data in our Solr statistics
|
||
<ul>
|
||
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
|
||
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
|
||
<li>I started processing those (about 411,000 records):</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>CGSpace DSpace 6 Upgrade</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</link>
|
||
<pubDate>Sun, 15 Nov 2020 13:27:35 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</guid>
|
||
<description><p>Notes about the DSpace 6 upgrade on CGSpace in 2020-11.</p></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>November, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-11/</link>
|
||
<pubDate>Sun, 01 Nov 2020 13:11:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-11/</guid>
|
||
<description><h2 id="2020-11-01">2020-11-01</h2>
|
||
<ul>
|
||
<li>Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
|
||
<ul>
|
||
<li>So far we&rsquo;ve spent at least fifty hours to process the statistics and statistics-2019 core&hellip; wow.</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>October, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-10/</link>
|
||
<pubDate>Tue, 06 Oct 2020 16:55:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-10/</guid>
|
||
<description><h2 id="2020-10-06">2020-10-06</h2>
|
||
<ul>
|
||
<li>Add tests for the new <code>/items</code> POST handlers to the DSpace 6.x branch of my <a href="https://github.com/ilri/dspace-statistics-api/tree/v6_x">dspace-statistics-api</a>
|
||
<ul>
|
||
<li>It took a bit of extra work because I had to learn how to mock the responses for when Solr is not available</li>
|
||
<li>Tag and release version 1.3.0 on GitHub: <a href="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0">https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
|
||
<ul>
|
||
<li>During the FlywayDB migration I got an error:</li>
|
||
</ul>
|
||
</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>September, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-09/</link>
|
||
<pubDate>Wed, 02 Sep 2020 15:35:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-09/</guid>
|
||
<description><h2 id="2020-09-02">2020-09-02</h2>
|
||
<ul>
|
||
<li>Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS</li>
|
||
<li>The AReS Explorer hasn&rsquo;t updated its index since 2020-08-22 when I last forced it
|
||
<ul>
|
||
<li>I restarted it again now and told Moayad that the automatic indexing isn&rsquo;t working</li>
|
||
</ul>
|
||
</li>
|
||
<li>Add <code>Alliance of Bioversity International and CIAT</code> to affiliations on CGSpace</li>
|
||
<li>Abenet told me that the general search text on AReS doesn&rsquo;t get reset when you use the &ldquo;Reset Filters&rdquo; button
|
||
<ul>
|
||
<li>I filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/39">https://github.com/ilri/OpenRXV/issues/39</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>I filed an issue on OpenRXV to make some minor edits to the admin UI: <a href="https://github.com/ilri/OpenRXV/issues/40">https://github.com/ilri/OpenRXV/issues/40</a></li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>August, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-08/</link>
|
||
<pubDate>Sun, 02 Aug 2020 15:35:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-08/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>July, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-07/</link>
|
||
<pubDate>Wed, 01 Jul 2020 10:53:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-07/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>June, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-06/</link>
|
||
<pubDate>Mon, 01 Jun 2020 13:55:39 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-06/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>May, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-05/</link>
|
||
<pubDate>Sat, 02 May 2020 09:52:04 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-05/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>April, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-04/</link>
|
||
<pubDate>Thu, 02 Apr 2020 10:53:24 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-04/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>March, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-03/</link>
|
||
<pubDate>Mon, 02 Mar 2020 12:31:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-03/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>February, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-02/</link>
|
||
<pubDate>Sun, 02 Feb 2020 11:56:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-02/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>January, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-01/</link>
|
||
<pubDate>Mon, 06 Jan 2020 10:48:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-01/</guid>
|
||
<description><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://hdl.handle.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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>December, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-12/</link>
|
||
<pubDate>Sun, 01 Dec 2019 11:22:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-12/</guid>
|
||
<description><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 tabindex="0"><code># apt update &amp;&amp; apt full-upgrade
|
||
# apt-get autoremove &amp;&amp; apt-get autoclean
|
||
# dpkg -C
|
||
# reboot
|
||
</code></pre></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>November, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-11/</link>
|
||
<pubDate>Mon, 04 Nov 2019 12:20:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-11/</guid>
|
||
<description><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 tabindex="0"><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>October, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-10/</link>
|
||
<pubDate>Tue, 01 Oct 2019 13:20:51 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-10/</guid>
|
||
<description>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.</description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>September, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-09/</link>
|
||
<pubDate>Sun, 01 Sep 2019 10:17:51 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-09/</guid>
|
||
<description><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>August, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-08/</link>
|
||
<pubDate>Sat, 03 Aug 2019 12:39:51 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-08/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>July, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-07/</link>
|
||
<pubDate>Mon, 01 Jul 2019 12:13:51 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-07/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>June, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-06/</link>
|
||
<pubDate>Sun, 02 Jun 2019 10:57:51 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-06/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>May, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-05/</link>
|
||
<pubDate>Wed, 01 May 2019 07:37:43 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-05/</guid>
|
||
<description><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>April, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-04/</link>
|
||
<pubDate>Mon, 01 Apr 2019 09:00:43 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-04/</guid>
|
||
<description><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 tabindex="0"><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 $9}' | sort | uniq -c | sort -n | tail -n 5
|
||
4432 200
|
||
</code></pre><ul>
|
||
<li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li>
|
||
<li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>$ ./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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>March, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-03/</link>
|
||
<pubDate>Fri, 01 Mar 2019 12:16:30 +0100</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-03/</guid>
|
||
<description><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% <20> 9.45 instead of 68.15% ± 9.45</li>
|
||
<li>2003<EFBFBD>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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>February, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-02/</link>
|
||
<pubDate>Fri, 01 Feb 2019 21:37:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-02/</guid>
|
||
<description><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 tabindex="0"><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>January, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-01/</link>
|
||
<pubDate>Wed, 02 Jan 2019 09:48:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-01/</guid>
|
||
<description><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>December, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-12/</link>
|
||
<pubDate>Sun, 02 Dec 2018 02:09:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-12/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>November, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-11/</link>
|
||
<pubDate>Thu, 01 Nov 2018 16:41:30 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-11/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>October, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-10/</link>
|
||
<pubDate>Mon, 01 Oct 2018 22:31:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-10/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>September, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-09/</link>
|
||
<pubDate>Sun, 02 Sep 2018 09:55:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-09/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>August, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-08/</link>
|
||
<pubDate>Wed, 01 Aug 2018 11:52:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-08/</guid>
|
||
<description><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>July, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-07/</link>
|
||
<pubDate>Sun, 01 Jul 2018 12:56:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-07/</guid>
|
||
<description><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 tabindex="0"><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 tabindex="0"><code>There is insufficient memory for the Java Runtime Environment to continue.
|
||
</code></pre></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>June, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-06/</link>
|
||
<pubDate>Mon, 04 Jun 2018 19:49:54 -0700</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-06/</guid>
|
||
<description><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 tabindex="0"><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>May, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-05/</link>
|
||
<pubDate>Tue, 01 May 2018 16:43:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-05/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>April, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-04/</link>
|
||
<pubDate>Sun, 01 Apr 2018 16:13:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-04/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>March, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-03/</link>
|
||
<pubDate>Fri, 02 Mar 2018 16:07:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-03/</guid>
|
||
<description><h2 id="2018-03-02">2018-03-02</h2>
|
||
<ul>
|
||
<li>Export a CSV of the IITA community metadata for Martin Mueller</li>
|
||
</ul></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>February, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-02/</link>
|
||
<pubDate>Thu, 01 Feb 2018 16:28:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-02/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>January, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-01/</link>
|
||
<pubDate>Tue, 02 Jan 2018 08:35:54 -0800</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-01/</guid>
|
||
<description><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 tabindex="0"><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 tabindex="0"><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>December, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-12/</link>
|
||
<pubDate>Fri, 01 Dec 2017 13:53:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-12/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>November, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-11/</link>
|
||
<pubDate>Thu, 02 Nov 2017 09:37:54 +0200</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-11/</guid>
|
||
<description><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 tabindex="0"><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>October, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-10/</link>
|
||
<pubDate>Sun, 01 Oct 2017 08:07:54 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-10/</guid>
|
||
<description><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 tabindex="0"><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></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>CGIAR Library Migration</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</link>
|
||
<pubDate>Mon, 18 Sep 2017 16:38:35 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</guid>
|
||
<description><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></description>
|
||
</item>
|
||
|
||
</channel>
|
||
</rss>
|