Add notes for 2018-01-03

content/post/2018-01.md

@@ -79,3 +79,109 @@ dspace.log.2018-01-02:34
 - Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let's Encrypt if it's just a handful of domains
 
 <!--more-->
+
+## 2018-01-03
+
+- I woke up to more up and down of CGSpace, this time UptimeRobot noticed a few rounds of up and down of a few minutes each and Linode also notified of high CPU load from 12 to 2 PM
+- Looks like I need to increase the database pool size again:
+
+```
+$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
+dspace.log.2018-01-01:0
+dspace.log.2018-01-02:1972
+dspace.log.2018-01-03:1909
+```
+
+- For some reason there were a lot of "active" connections last night:
+
+![CGSpace PostgreSQL connections](/cgspace-notes/2018/01/postgres_connections-day.png)
+
+- The active IPs in XMLUI are:
+
+```
+# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
+    607 40.77.167.141
+    611 2a00:23c3:8c94:7800:392c:a491:e796:9c50
+    663 188.226.169.37
+    759 157.55.39.245
+    887 68.180.229.254
+   1037 157.55.39.175
+   1068 216.244.66.245
+   1495 66.249.64.91
+   1934 104.196.152.243
+   2219 134.155.96.78
+```
+
+- 134.155.96.78 appears to be at the University of Mannheim in Germany
+- They identify as: Mozilla/5.0 (compatible; heritrix/3.2.0 +http://ifm.uni-mannheim.de)
+- This appears to be the [Internet Archive's open source bot](https://github.com/internetarchive/heritrix3)
+- They seem to be re-using their Tomcat session so I don't need to do anything to them just yet:
+
+```
+$ grep 134.155.96.78 dspace.log.2018-01-03 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
+2
+```
+
+- The API logs show the normal users:
+
+```
+# cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
+     32 207.46.13.182
+     38 40.77.167.132
+     38 68.180.229.254
+     43 66.249.64.91
+     46 40.77.167.141
+     49 157.55.39.245
+     79 157.55.39.175
+   1533 50.116.102.77
+   4069 70.32.83.92
+   9355 45.5.184.196
+```
+
+- In other related news I see a sizeable amount of requests coming from python-requests
+- For example, just in the last day there were 1700!
+
+```
+# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -c python-requests
+1773
+```
+
+- But they come from hundreds of IPs, many of which are 54.x.x.x:
+
+```
+# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep python-requests | awk '{print $1}' | sort -n | uniq -c | sort -h | tail -n 30
+      9 54.144.87.92
+      9 54.146.222.143
+      9 54.146.249.249
+      9 54.158.139.206
+      9 54.161.235.224
+      9 54.163.41.19
+      9 54.163.4.51
+      9 54.196.195.107
+      9 54.198.89.134
+      9 54.80.158.113
+     10 54.198.171.98
+     10 54.224.53.185
+     10 54.226.55.207
+     10 54.227.8.195
+     10 54.242.234.189
+     10 54.242.238.209
+     10 54.80.100.66
+     11 54.161.243.121
+     11 54.205.154.178
+     11 54.234.225.84
+     11 54.87.23.173
+     11 54.90.206.30
+     12 54.196.127.62
+     12 54.224.242.208
+     12 54.226.199.163
+     13 54.162.149.249
+     13 54.211.182.255
+     19 50.17.61.150
+     21 54.211.119.107
+    139 164.39.7.62
+```
+
+- I have no idea what these are but they seem to be coming from Amazon...
+- I guess for now I just have to increase the database connection pool's max active
+- It's currently 75 and normally I'd just bump it by 25 but let me be a bit daring and push it by 50 to 125, because I used to see at least 121 connections in pg_stat_activity before when we were using the shitty default pooling

public/2015-11/index.html

@@ -52,7 +52,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac
 
 
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public/2015-12/index.html

@@ -54,7 +54,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
 
 
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+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-01/index.html

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public/2016-02/index.html

@@ -58,7 +58,7 @@ Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE&r
 
 
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+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-03/index.html

@@ -44,7 +44,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-04/index.html

@@ -48,7 +48,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-05/index.html

@@ -52,7 +52,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-06/index.html

@@ -50,7 +50,7 @@ Working on second phase of metadata migration, looks like this will work for mov
 
 
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+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-07/index.html

@@ -66,7 +66,7 @@ In this case the select query was showing 95 results before the update
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-08/index.html

@@ -60,7 +60,7 @@ $ git rebase -i dspace-5.5
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-09/index.html

@@ -52,7 +52,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=or
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-10/index.html

@@ -60,7 +60,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-11/index.html

@@ -44,7 +44,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2016-12/index.html

@@ -68,7 +68,7 @@ Another worrying error from dspace.log is:
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-01/index.html

@@ -44,7 +44,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
 
 
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+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-02/index.html

@@ -72,7 +72,7 @@ Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-03/index.html

@@ -76,7 +76,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-04/index.html

@@ -62,7 +62,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Th
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-05/index.html

@@ -28,7 +28,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="May, 2017"/>
 <meta name="twitter:description" content="2017-05-01  ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items:  https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683   2017-05-02  Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request  2017-05-04  Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-06/index.html

@@ -28,7 +28,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="June, 2017"/>
 <meta name="twitter:description" content="2017-06-01  After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-07/index.html

@@ -56,7 +56,7 @@ We can use PostgreSQL’s extended output format (-x) plus sed to format the
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-08/index.html

@@ -76,7 +76,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-09/index.html

@@ -52,7 +52,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account
 
 
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-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-10/index.html

@@ -56,7 +56,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
 
 
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+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-11/index.html

@@ -76,7 +76,7 @@ COPY 54701
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2017-12/index.html

@@ -46,7 +46,7 @@ The list of connections to XMLUI and REST API for today:
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/2018-01/index.html

@@ -184,7 +184,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
 
 
 "/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     
@@ -194,7 +194,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
   "@type": "BlogPosting",
   "headline": "January, 2018",
   "url": "https://alanorth.github.io/cgspace-notes/2018-01/",
-  "wordCount": "282",
+  "wordCount": "731",
   "datePublished": "2018-01-02T08:35:54-08:00",
   "dateModified": "2018-01-02T09:30:34-08:00",
   "author": {
@@ -339,6 +339,122 @@ dspace.log.2018-01-02:34
 
 <p></p>
 
+<h2 id="2018-01-03">2018-01-03</h2>
+
+<ul>
+<li>I woke up to more up and down of CGSpace, this time UptimeRobot noticed a few rounds of up and down of a few minutes each and Linode also notified of high CPU load from 12 to 2 PM</li>
+<li>Looks like I need to increase the database pool size again:</li>
+</ul>
+
+<pre><code>$ grep -c &quot;Timeout: Pool empty.&quot; dspace.log.2018-01-*
+dspace.log.2018-01-01:0
+dspace.log.2018-01-02:1972
+dspace.log.2018-01-03:1909
+</code></pre>
+
+<ul>
+<li>For some reason there were a lot of &ldquo;active&rdquo; connections last night:</li>
+</ul>
+
+<p><img src="/cgspace-notes/2018/01/postgres_connections-day.png" alt="CGSpace PostgreSQL connections" /></p>
+
+<ul>
+<li>The active IPs in XMLUI are:</li>
+</ul>
+
+<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E &quot;3/Jan/2018&quot; | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
+    607 40.77.167.141
+    611 2a00:23c3:8c94:7800:392c:a491:e796:9c50
+    663 188.226.169.37
+    759 157.55.39.245
+    887 68.180.229.254
+   1037 157.55.39.175
+   1068 216.244.66.245
+   1495 66.249.64.91
+   1934 104.196.152.243
+   2219 134.155.96.78
+</code></pre>
+
+<ul>
+<li>134.155.96.78 appears to be at the University of Mannheim in Germany</li>
+<li>They identify as: Mozilla/5.0 (compatible; heritrix/3.2.0 +<a href="http://ifm.uni-mannheim.de">http://ifm.uni-mannheim.de</a>)</li>
+<li>This appears to be the <a href="https://github.com/internetarchive/heritrix3">Internet Archive&rsquo;s open source bot</a></li>
+<li>They seem to be re-using their Tomcat session so I don&rsquo;t need to do anything to them just yet:</li>
+</ul>
+
+<pre><code>$ grep 134.155.96.78 dspace.log.2018-01-03 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
+2
+</code></pre>
+
+<ul>
+<li>The API logs show the normal users:</li>
+</ul>
+
+<pre><code># cat /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;3/Jan/2018&quot; | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
+     32 207.46.13.182
+     38 40.77.167.132
+     38 68.180.229.254
+     43 66.249.64.91
+     46 40.77.167.141
+     49 157.55.39.245
+     79 157.55.39.175
+   1533 50.116.102.77
+   4069 70.32.83.92
+   9355 45.5.184.196
+</code></pre>
+
+<ul>
+<li>In other related news I see a sizeable amount of requests coming from python-requests</li>
+<li>For example, just in the last day there were 1700!</li>
+</ul>
+
+<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -c python-requests
+1773
+</code></pre>
+
+<ul>
+<li>But they come from hundreds of IPs, many of which are 54.x.x.x:</li>
+</ul>
+
+<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep python-requests | awk '{print $1}' | sort -n | uniq -c | sort -h | tail -n 30
+      9 54.144.87.92
+      9 54.146.222.143
+      9 54.146.249.249
+      9 54.158.139.206
+      9 54.161.235.224
+      9 54.163.41.19
+      9 54.163.4.51
+      9 54.196.195.107
+      9 54.198.89.134
+      9 54.80.158.113
+     10 54.198.171.98
+     10 54.224.53.185
+     10 54.226.55.207
+     10 54.227.8.195
+     10 54.242.234.189
+     10 54.242.238.209
+     10 54.80.100.66
+     11 54.161.243.121
+     11 54.205.154.178
+     11 54.234.225.84
+     11 54.87.23.173
+     11 54.90.206.30
+     12 54.196.127.62
+     12 54.224.242.208
+     12 54.226.199.163
+     13 54.162.149.249
+     13 54.211.182.255
+     19 50.17.61.150
+     21 54.211.119.107
+    139 164.39.7.62
+</code></pre>
+
+<ul>
+<li>I have no idea what these are but they seem to be coming from Amazon&hellip;</li>
+<li>I guess for now I just have to increase the database connection pool&rsquo;s max active</li>
+<li>It&rsquo;s currently 75 and normally I&rsquo;d just bump it by 25 but let me be a bit daring and push it by 50 to 125, because I used to see at least 121 connections in pg_stat_activity before when we were using the shitty default pooling</li>
+</ul>
+
   
 
   

public/categories/notes/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/cgiar-library-migration/index.html

@@ -28,7 +28,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="CGIAR Library Migration"/>
 <meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="CGSpace Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/page/2/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="CGSpace Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/page/3/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="CGSpace Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/post/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Posts"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/post/page/2/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Posts"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/post/page/3/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Posts"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/robots.txt

@@ -31,7 +31,7 @@ Disallow: /cgspace-notes/2015-12/
 Disallow: /cgspace-notes/2015-11/
 Disallow: /cgspace-notes/
 Disallow: /cgspace-notes/categories/
-Disallow: /cgspace-notes/categories/notes/
 Disallow: /cgspace-notes/tags/notes/
+Disallow: /cgspace-notes/categories/notes/
 Disallow: /cgspace-notes/post/
 Disallow: /cgspace-notes/tags/

public/sitemap.xml

@@ -154,14 +154,14 @@
   </url>
   
   <url>
-    <loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
+    <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
-    <lastmod>2017-09-28T12:00:49+03:00</lastmod>
+    <lastmod>2018-01-02T09:30:34-08:00</lastmod>
     <priority>0</priority>
   </url>
   
   <url>
-    <loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
+    <loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
-    <lastmod>2018-01-02T09:30:34-08:00</lastmod>
+    <lastmod>2017-09-28T12:00:49+03:00</lastmod>
     <priority>0</priority>
   </url>
   

public/tags/notes/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/tags/notes/page/2/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />
 
 
     

public/tags/notes/page/3/index.html

@@ -25,7 +25,7 @@
 
 <meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.32.1" />
+<meta name="generator" content="Hugo 0.32.2" />