Add notes for 2016-02-09

Signed-off-by: Alan Orth <alan.orth@gmail.com>

content/2016-02.md

@@ -109,3 +109,48 @@ $ ~/dspace/bin/dspace index-discovery -b
 
 ![ILRI submission buttons](../images/2016/02/submit-button-ilri.png)
 ![Drylands submission buttons](../images/2016/02/submit-button-drylands.png)
+
+## 2016-02-09
+
+- Re-sync DSpace Test with CGSpace
+- Help Sisay with OpenRefine
+- Enable HTTPS on DSpace Test using Let's Encrypt:
+
+```
+$ cd ~/src/git
+$ git clone https://github.com/letsencrypt/letsencrypt
+$ cd letsencrypt
+$ sudo service nginx stop
+# add port 443 to firewall rules
+$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
+$ sudo service nginx start
+$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
+```
+
+- We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: https://letsencrypt.org/howitworks/
+- I had to export some CIAT items that were being cleaned up on the test server and I noticed their `dc.contributor.author` fields have DSpace 5 authority index UUIDs...
+- To clean those up in OpenRefine I used this GREL expression: `value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")`
+- Getting more and more hangs on DSpace Test, seemingly random but also during CSV import
+- Logs don't always show anything right when it fails, but eventually one of these appears:
+
+```
+org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
+```
+
+- or
+
+```
+Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
+```
+
+- Right now DSpace Test's Tomcat heap is set to 1536m and we have quite a bit of free RAM:
+
+```
+# free -m
+             total       used       free     shared    buffers     cached
+Mem:          3950       3902         48          9         37       1311
+-/+ buffers/cache:       2552       1397
+Swap:          255         57        198
+```
+
+- So I'll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)

public/2016-02/index.html

@@ -199,6 +199,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
 <p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
 <img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
 
+<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
+
+<ul>
+<li>Re-sync DSpace Test with CGSpace</li>
+<li>Help Sisay with OpenRefine</li>
+<li>Enable HTTPS on DSpace Test using Let&rsquo;s Encrypt:</li>
+</ul>
+
+<pre><code>$ cd ~/src/git
+$ git clone https://github.com/letsencrypt/letsencrypt
+$ cd letsencrypt
+$ sudo service nginx stop
+# add port 443 to firewall rules
+$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
+$ sudo service nginx start
+$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
+</code></pre>
+
+<ul>
+<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
+<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs&hellip;</li>
+<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,&quot;&quot;)</code></li>
+<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
+<li>Logs don&rsquo;t always show anything right when it fails, but eventually one of these appears:</li>
+</ul>
+
+<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
+</code></pre>
+
+<ul>
+<li>or</li>
+</ul>
+
+<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
+</code></pre>
+
+<ul>
+<li>Right now DSpace Test&rsquo;s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
+</ul>
+
+<pre><code># free -m
+             total       used       free     shared    buffers     cached
+Mem:          3950       3902         48          9         37       1311
+-/+ buffers/cache:       2552       1397
+Swap:          255         57        198
+</code></pre>
+
+<ul>
+<li>So I&rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
+</ul>
+
   </section>
   <footer>
     

public/index.xml

@@ -136,6 +136,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
 
 <p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
 <img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
+
+<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
+
+<ul>
+<li>Re-sync DSpace Test with CGSpace</li>
+<li>Help Sisay with OpenRefine</li>
+<li>Enable HTTPS on DSpace Test using Let’s Encrypt:</li>
+</ul>
+
+<pre><code>$ cd ~/src/git
+$ git clone https://github.com/letsencrypt/letsencrypt
+$ cd letsencrypt
+$ sudo service nginx stop
+# add port 443 to firewall rules
+$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
+$ sudo service nginx start
+$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
+</code></pre>
+
+<ul>
+<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
+<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs…</li>
+<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li>
+<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
+<li>Logs don’t always show anything right when it fails, but eventually one of these appears:</li>
+</ul>
+
+<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
+</code></pre>
+
+<ul>
+<li>or</li>
+</ul>
+
+<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
+</code></pre>
+
+<ul>
+<li>Right now DSpace Test’s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
+</ul>
+
+<pre><code># free -m
+             total       used       free     shared    buffers     cached
+Mem:          3950       3902         48          9         37       1311
+-/+ buffers/cache:       2552       1397
+Swap:          255         57        198
+</code></pre>
+
+<ul>
+<li>So I’ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
+</ul>
 </description>
     </item>
     

public/tags/notes/index.xml

@@ -136,6 +136,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
 
 <p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" />
 <img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p>
+
+<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2>
+
+<ul>
+<li>Re-sync DSpace Test with CGSpace</li>
+<li>Help Sisay with OpenRefine</li>
+<li>Enable HTTPS on DSpace Test using Let’s Encrypt:</li>
+</ul>
+
+<pre><code>$ cd ~/src/git
+$ git clone https://github.com/letsencrypt/letsencrypt
+$ cd letsencrypt
+$ sudo service nginx stop
+# add port 443 to firewall rules
+$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
+$ sudo service nginx start
+$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
+</code></pre>
+
+<ul>
+<li>We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: <a href="https://letsencrypt.org/howitworks/">https://letsencrypt.org/howitworks/</a></li>
+<li>I had to export some CIAT items that were being cleaned up on the test server and I noticed their <code>dc.contributor.author</code> fields have DSpace 5 authority index UUIDs…</li>
+<li>To clean those up in OpenRefine I used this GREL expression: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li>
+<li>Getting more and more hangs on DSpace Test, seemingly random but also during CSV import</li>
+<li>Logs don’t always show anything right when it fails, but eventually one of these appears:</li>
+</ul>
+
+<pre><code>org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
+</code></pre>
+
+<ul>
+<li>or</li>
+</ul>
+
+<pre><code>Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
+</code></pre>
+
+<ul>
+<li>Right now DSpace Test’s Tomcat heap is set to 1536m and we have quite a bit of free RAM:</li>
+</ul>
+
+<pre><code># free -m
+             total       used       free     shared    buffers     cached
+Mem:          3950       3902         48          9         37       1311
+-/+ buffers/cache:       2552       1397
+Swap:          255         57        198
+</code></pre>
+
+<ul>
+<li>So I’ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li>
+</ul>
 </description>
     </item>