Add notes for 2020-11-15

content/posts/2020-11.md

@@ -127,6 +127,8 @@ dspace=# COMMIT;
 - I did some tests to add a usage statistics chart to the item views on DSpace Test
   - It is inspired by Salem's work on WorldFish's repository, and it hits the dspace-statistics-api for the current item and displays a graph
   - I got it working very easily for all-time statistics with Chart.js, but I think I will need to use Highcharts or something else because Chart.js is HTML5 canvas and doesn't allow theming via CSS (so our Bootstrap brand colors for each theme won't work)
+    - Hmm, Highcharts is not licensed under and open source license so I will not use it
+    - Perhaps I'll use Chartist with the popover plugin...
   - I think I'll pursue this after the DSpace 6 upgrade...
 
 ## 2020-11-12
@@ -155,4 +157,53 @@ facet=true&facet.field=owningComm&facet.mincount=1&facet.limit=100&facet.offset=
   - I hadn't seen monit before, but the others are already in DSpace's spider agents lists for some time so probably only appear in older stats cores
   - The issue with purging these using `check-spider-hits.sh` is that it can't do case-insensitive regexes and some metacharacters like `\s` don't work so I added case-sensitive patterns to a local agents file and purged them with the script
 
+## 2020-11-15
+
+- Upgrade CGSpace to DSpace 6.3
+  - First build, update, and migrate the database:
+
+```
+$ dspace cleanup -v
+$ git checkout origin/6_x-dev-atmire-modules
+$ npm install -g yarn
+$ chrt -b 0 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2,\!dspace-jspui clean package
+$ sudo su - postgres
+$ psql dspace -c 'CREATE EXTENSION pgcrypto;'
+$ psql dspace -c "DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');"
+$ exit
+$ rm -rf /home/cgspace/config/spring
+$ ant update
+$ dspace database info
+$ dspace database migrate
+$ sudo systemctl start tomcat7
+```
+
+- After starting Tomcat DSpace should start up OK and begin Discovery indexing, but I want to also upgrade from PostgreSQL 9.6 to 10
+  - I installed and configured PostgreSQL 10 using the Ansible playbooks, then migrated the database manually:
+
+```
+# systemctl stop tomcat7
+# pg_ctlcluster 9.6 main stop
+# tar -cvzpf var-lib-postgresql-9.6.tar.gz /var/lib/postgresql/9.6
+# tar -cvzpf etc-postgresql-9.6.tar.gz /etc/postgresql/9.6
+# pg_ctlcluster 10 main stop
+# pg_dropcluster 10 main
+# pg_upgradecluster 9.6 main
+# pg_dropcluster 9.6 main
+# systemctl start postgresql
+# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r
+```
+
+- Then I ran all system updates and rebooted the server...
+- After the server came back up I re-ran the Ansible playbook to make sure all configs and services were updated
+- I disabled the dspace-statistsics-api for now because it won't work until I migrate all the Solr statistics anyways
+- Start a full Discovery re-indexing:
+
+```
+$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
+```
+
+- I updated all the Ansible infrastructure and DSpace branches to be the DSpace 6 ones
+- I will wait until the Discovery indexing is finished to start doing the Solr statistics migration
+
 <!-- vim: set sw=2 ts=2: -->

docs/2020-11/index.html

@@ -17,7 +17,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-11/" />
 <meta property="article:published_time" content="2020-11-01T13:11:54+02:00" />
-<meta property="article:modified_time" content="2020-11-10T17:00:02+02:00" />
+<meta property="article:modified_time" content="2020-11-13T09:22:18+02:00" />
 
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="November, 2020"/>
@@ -39,9 +39,9 @@ So far we&rsquo;ve spent at least fifty hours to process the statistics and stat
   "@type": "BlogPosting",
   "headline": "November, 2020",
   "url": "https://alanorth.github.io/cgspace-notes/2020-11/",
-  "wordCount": "1266",
+  "wordCount": "1565",
   "datePublished": "2020-11-01T13:11:54+02:00",
-  "dateModified": "2020-11-10T17:00:02+02:00",
+  "dateModified": "2020-11-13T09:22:18+02:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -257,7 +257,12 @@ dspace=# COMMIT;
 <li>I did some tests to add a usage statistics chart to the item views on DSpace Test
 <ul>
 <li>It is inspired by Salem&rsquo;s work on WorldFish&rsquo;s repository, and it hits the dspace-statistics-api for the current item and displays a graph</li>
-<li>I got it working very easily for all-time statistics with Chart.js, but I think I will need to use Highcharts or something else because Chart.js is HTML5 canvas and doesn&rsquo;t allow theming via CSS (so our Bootstrap brand colors for each theme won&rsquo;t work)</li>
+<li>I got it working very easily for all-time statistics with Chart.js, but I think I will need to use Highcharts or something else because Chart.js is HTML5 canvas and doesn&rsquo;t allow theming via CSS (so our Bootstrap brand colors for each theme won&rsquo;t work)
+<ul>
+<li>Hmm, Highcharts is not licensed under and open source license so I will not use it</li>
+<li>Perhaps I&rsquo;ll use Chartist with the popover plugin&hellip;</li>
+</ul>
+</li>
 <li>I think I&rsquo;ll pursue this after the DSpace 6 upgrade&hellip;</li>
 </ul>
 </li>
@@ -293,6 +298,55 @@ dspace=# COMMIT;
 </ul>
 </li>
 </ul>
+<h2 id="2020-11-15">2020-11-15</h2>
+<ul>
+<li>Upgrade CGSpace to DSpace 6.3
+<ul>
+<li>First build, update, and migrate the database:</li>
+</ul>
+</li>
+</ul>
+<pre><code>$ dspace cleanup -v
+$ git checkout origin/6_x-dev-atmire-modules
+$ npm install -g yarn
+$ chrt -b 0 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2,\!dspace-jspui clean package
+$ sudo su - postgres
+$ psql dspace -c 'CREATE EXTENSION pgcrypto;'
+$ psql dspace -c &quot;DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');&quot;
+$ exit
+$ rm -rf /home/cgspace/config/spring
+$ ant update
+$ dspace database info
+$ dspace database migrate
+$ sudo systemctl start tomcat7
+</code></pre><ul>
+<li>After starting Tomcat DSpace should start up OK and begin Discovery indexing, but I want to also upgrade from PostgreSQL 9.6 to 10
+<ul>
+<li>I installed and configured PostgreSQL 10 using the Ansible playbooks, then migrated the database manually:</li>
+</ul>
+</li>
+</ul>
+<pre><code># systemctl stop tomcat7
+# pg_ctlcluster 9.6 main stop
+# tar -cvzpf var-lib-postgresql-9.6.tar.gz /var/lib/postgresql/9.6
+# tar -cvzpf etc-postgresql-9.6.tar.gz /etc/postgresql/9.6
+# pg_ctlcluster 10 main stop
+# pg_dropcluster 10 main
+# pg_upgradecluster 9.6 main
+# pg_dropcluster 9.6 main
+# systemctl start postgresql
+# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r
+</code></pre><ul>
+<li>Then I ran all system updates and rebooted the server&hellip;</li>
+<li>After the server came back up I re-ran the Ansible playbook to make sure all configs and services were updated</li>
+<li>I disabled the dspace-statistsics-api for now because it won&rsquo;t work until I migrate all the Solr statistics anyways</li>
+<li>Start a full Discovery re-indexing:</li>
+</ul>
+<pre><code>$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
+</code></pre><ul>
+<li>I updated all the Ansible infrastructure and DSpace branches to be the DSpace 6 ones</li>
+<li>I will wait until the Discovery indexing is finished to start doing the Solr statistics migration</li>
+</ul>
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docs/categories/index.html

@@ -9,7 +9,7 @@
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docs/categories/notes/index.html

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docs/categories/notes/page/2/index.html

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docs/categories/notes/page/4/index.html

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docs/index.html

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