Add notes for 2019-12-17

docs/2018-07/index.html

@@ -33,7 +33,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r
 
 There is insufficient memory for the Java Runtime Environment to continue.
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@@ -114,7 +114,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
 
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-  <h2 id="20180701">2018-07-01</h2>
+  <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>
@@ -147,12 +147,12 @@ $ dspace database migrate ignored
 </code></pre><ul>
 <li>After that I started Tomcat 7 and DSpace seems to be working, now I need to tell our colleagues to try stuff and report issues they have</li>
 </ul>
-<h2 id="20180702">2018-07-02</h2>
+<h2 id="2018-07-02">2018-07-02</h2>
 <ul>
 <li>Discuss AgriKnowledge including our Handle identifier on their harvested items from CGSpace</li>
 <li>They seem to be only interested in Gates-funded outputs, for example: <a href="https://www.agriknowledge.org/files/tm70mv21t">https://www.agriknowledge.org/files/tm70mv21t</a></li>
 </ul>
-<h2 id="20180703">2018-07-03</h2>
+<h2 id="2018-07-03">2018-07-03</h2>
 <ul>
 <li>Finally finish with the CIFOR Archive records (a total of 2448):
 <ul>
@@ -213,7 +213,7 @@ Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Mana
 </code></pre><ul>
 <li>Gotta check that out later&hellip;</li>
 </ul>
-<h2 id="20180704">2018-07-04</h2>
+<h2 id="2018-07-04">2018-07-04</h2>
 <ul>
 <li>I verified that the autowire error indeed only occurs on Tomcat 8.5, but the application works fine on Tomcat 7</li>
 <li>I have raised this in the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 compatibility ticket on Atmire's tracker</a></li>
@@ -221,12 +221,12 @@ Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Mana
 <li>Also, Udana wants me to add &ldquo;Enhancing Sustainability Across Agricultural Systems&rdquo; to the WLE Phase II research themes so I created a ticket to track that (<a href="https://github.com/ilri/DSpace/issues/382">#382</a>)</li>
 <li>I need to try to finish this DSpace 5.8 business first because I have too many branches with cherry-picks going on right now!</li>
 </ul>
-<h2 id="20180706">2018-07-06</h2>
+<h2 id="2018-07-06">2018-07-06</h2>
 <ul>
 <li>CCAFS want me to add &ldquo;PII-FP2_MSCCCAFS&rdquo; to their Phase II project tags on CGSpace (<a href="https://github.com/ilri/DSpace/issues/383">#383</a>)</li>
 <li>I'll do it in a batch with all the other metadata updates next week</li>
 </ul>
-<h2 id="20180708">2018-07-08</h2>
+<h2 id="2018-07-08">2018-07-08</h2>
 <ul>
 <li>I was tempted to do the Linode instance upgrade on CGSpace (linode18), but after looking closely at the system backups I noticed that Solr isn't being backed up to S3</li>
 <li>I apparently noticed this—and fixed it!—in <a href="/cgspace-notes/2016-07/">2016-07</a>, but it doesn't look like the backup has been updated since then!</li>
@@ -246,7 +246,7 @@ $ ./resolve-orcids.py -i /tmp/2018-07-08-orcids.txt -o /tmp/2018-07-08-names.txt
 </code></pre><ul>
 <li>But after comparing to the existing list of names I didn't see much change, so I just ignored it</li>
 </ul>
-<h2 id="20180709">2018-07-09</h2>
+<h2 id="2018-07-09">2018-07-09</h2>
 <ul>
 <li>Uptime Robot said that CGSpace was down for two minutes early this morning but I don't see anything in Tomcat logs or dmesg</li>
 <li>Uptime Robot said that CGSpace was down for two minutes again later in the day, and this time I saw a memory error in Tomcat's <code>catalina.out</code>:</li>
@@ -295,7 +295,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
 <li>Interestingly, the first time that I see <code>35.227.26.162</code> was on 2018-06-08</li>
 <li>I've added <code>35.227.26.162</code> to the bot tagging logic in the nginx vhost</li>
 </ul>
-<h2 id="20180710">2018-07-10</h2>
+<h2 id="2018-07-10">2018-07-10</h2>
 <ul>
 <li>Add &ldquo;United Kingdom government&rdquo; to sponsors (<a href="https://github.com/ilri/DSpace/issues/381">#381</a>)</li>
 <li>Add &ldquo;Enhancing Sustainability Across Agricultural Systems&rdquo; to WLE Phase II Research Themes (<a href="https://github.com/ilri/DSpace/issues/382">#382</a>)</li>
@@ -325,7 +325,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
 <li>He said there was a bug that caused his app to request a bunch of invalid URLs</li>
 <li>I'll have to keep and eye on this and see how their platform evolves</li>
 </ul>
-<h2 id="20180711">2018-07-11</h2>
+<h2 id="2018-07-11">2018-07-11</h2>
 <ul>
 <li>Skype meeting with Peter and Addis CGSpace team
 <ul>
@@ -336,7 +336,7 @@ org.apache.solr.client.solrj.SolrServerException: IOException occured when talki
 </ul>
 </li>
 </ul>
-<h2 id="20180712">2018-07-12</h2>
+<h2 id="2018-07-12">2018-07-12</h2>
 <ul>
 <li>Uptime Robot said that CGSpace went down a few times last night, around 10:45 PM and 12:30 AM</li>
 <li>Here are the top ten IPs from last night and this morning:</li>
@@ -396,13 +396,13 @@ $ csvcut -c 1 &lt; /tmp/affiliations.csv &gt; /tmp/affiliations-1.csv
 </code></pre><ul>
 <li>We also need to discuss standardizing our countries and comparing our ORCID iDs</li>
 </ul>
-<h2 id="20180713">2018-07-13</h2>
+<h2 id="2018-07-13">2018-07-13</h2>
 <ul>
 <li>Generate a list of affiliations for Peter and Abenet to go over so we can batch correct them before we deploy the new data visualization dashboard:</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 = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv header;
 COPY 4518
-</code></pre><h2 id="20180715">2018-07-15</h2>
+</code></pre><h2 id="2018-07-15">2018-07-15</h2>
 <ul>
 <li>Run all system updates on CGSpace, add latest metadata changes from last week, and start the Linode instance upgrade</li>
 <li>After the upgrade I see we have more disk space available in the instance's dashboard, so I shut the instance down and resized it from 392GB to 650GB</li>
@@ -447,7 +447,7 @@ $ ./resolve-orcids.py -i /tmp/2018-07-15-orcid-ids.txt -o /tmp/2018-07-15-resolv
 <li>I will check with the CGSpace team to see if they want me to add these to CGSpace</li>
 <li>Help Udana from WLE understand some Altmetrics concepts</li>
 </ul>
-<h2 id="20180718">2018-07-18</h2>
+<h2 id="2018-07-18">2018-07-18</h2>
 <ul>
 <li>ICARDA sent me another refined list of ORCID iDs so I sorted and formatted them into our controlled vocabulary again</li>
 <li>Participate in call with IWMI and WLE to discuss Altmetric, CGSpace, and social media</li>
@@ -486,7 +486,7 @@ Vary: Accept-Encoding
 X-Content-Type-Options: nosniff
 X-Frame-Options: SAMEORIGIN
 X-XSS-Protection: 1; mode=block
-</code></pre><h2 id="20180719">2018-07-19</h2>
+</code></pre><h2 id="2018-07-19">2018-07-19</h2>
 <ul>
 <li>I tested a submission via SAF bundle to DSpace 5.8 and it worked fine</li>
 <li>In addition to testing DSpace 5.8, I specifically wanted to see if the issue with specifying collections in metadata instead of on the command line would work (<a href="https://jira.duraspace.org/browse/DS-3583">DS-3583</a>)</li>
@@ -497,7 +497,7 @@ X-XSS-Protection: 1; mode=block
 <li>I told her that they need to start using more accurate dates for their issue dates</li>
 <li>In the example item I looked at the DOI has a publish date of 2018-03-16, so they should really try to capture that</li>
 </ul>
-<h2 id="20180722">2018-07-22</h2>
+<h2 id="2018-07-22">2018-07-22</h2>
 <ul>
 <li>I told the IWMI people that they can use <code>sort_by=3</code> in their OpenSearch query to sort the results by <code>dc.date.accessioned</code> instead of <code>dc.date.issued</code></li>
 <li>They say that it is a burden for them to capture the issue dates, so I cautioned them that this is in their own benefit for future posterity and that everyone else on CGSpace manages to capture the issue dates!</li>
@@ -510,7 +510,7 @@ X-XSS-Protection: 1; mode=block
 <li>I finally informed Atmire that we're ready to proceed with deploying this to CGSpace and that they should advise whether we should wait about the SNAPSHOT versions in <code>pom.xml</code></li>
 <li>There is no word on the issue I reported with Tomcat 8.5.32 yet, though&hellip;</li>
 </ul>
-<h2 id="20180723">2018-07-23</h2>
+<h2 id="2018-07-23">2018-07-23</h2>
 <ul>
 <li>Still discussing dates with IWMI</li>
 <li>I looked in the database to see the breakdown of date formats used in <code>dc.date.issued</code>, ie YYYY, YYYY-MM, or YYYY-MM-DD:</li>
@@ -532,11 +532,11 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
 </code></pre><ul>
 <li>So it looks like YYYY is the most numerious, followed by YYYY-MM-DD, then YYYY-MM</li>
 </ul>
-<h2 id="20180726">2018-07-26</h2>
+<h2 id="2018-07-26">2018-07-26</h2>
 <ul>
 <li>Run system updates on DSpace Test (linode19) and reboot the server</li>
 </ul>
-<h2 id="20180727">2018-07-27</h2>
+<h2 id="2018-07-27">2018-07-27</h2>
 <ul>
 <li>Follow up with Atmire again about the SNAPSHOT versions in our <code>pom.xml</code> because I want to finalize the DSpace 5.8 upgrade soon and I haven't heard from them in a month (<a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">ticket 560</a>)</li>
 </ul>