Add notes for 2016-02-09

Signed-off-by: Alan Orth <alan.orth@gmail.com>
This commit is contained in:
Alan Orth 2016-02-09 18:21:55 +02:00
parent 86ffcfd656
commit 380ca762af
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
4 changed files with 198 additions and 0 deletions

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@ -109,3 +109,48 @@ $ ~/dspace/bin/dspace index-discovery -b
![ILRI submission buttons](../images/2016/02/submit-button-ilri.png) ![ILRI submission buttons](../images/2016/02/submit-button-ilri.png)
![Drylands submission buttons](../images/2016/02/submit-button-drylands.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)

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@ -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" /> <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> <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> </section>
<footer> <footer>

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@ -136,6 +136,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
&lt;p&gt;&lt;img src=&#34;../images/2016/02/submit-button-ilri.png&#34; alt=&#34;ILRI submission buttons&#34; /&gt; &lt;p&gt;&lt;img src=&#34;../images/2016/02/submit-button-ilri.png&#34; alt=&#34;ILRI submission buttons&#34; /&gt;
&lt;img src=&#34;../images/2016/02/submit-button-drylands.png&#34; alt=&#34;Drylands submission buttons&#34; /&gt;&lt;/p&gt; &lt;img src=&#34;../images/2016/02/submit-button-drylands.png&#34; alt=&#34;Drylands submission buttons&#34; /&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-02-09:124a59adbaa8ef13e1518d003fc03981&#34;&gt;2016-02-09&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Re-sync DSpace Test with CGSpace&lt;/li&gt;
&lt;li&gt;Help Sisay with OpenRefine&lt;/li&gt;
&lt;li&gt;Enable HTTPS on DSpace Test using Let&amp;rsquo;s Encrypt:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;$ 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
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;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: &lt;a href=&#34;https://letsencrypt.org/howitworks/&#34;&gt;https://letsencrypt.org/howitworks/&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;I had to export some CIAT items that were being cleaned up on the test server and I noticed their &lt;code&gt;dc.contributor.author&lt;/code&gt; fields have DSpace 5 authority index UUIDs&amp;hellip;&lt;/li&gt;
&lt;li&gt;To clean those up in OpenRefine I used this GREL expression: &lt;code&gt;value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,&amp;quot;&amp;quot;)&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Getting more and more hangs on DSpace Test, seemingly random but also during CSV import&lt;/li&gt;
&lt;li&gt;Logs don&amp;rsquo;t always show anything right when it fails, but eventually one of these appears:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;or&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Right now DSpace Test&amp;rsquo;s Tomcat heap is set to 1536m and we have quite a bit of free RAM:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;# free -m
total used free shared buffers cached
Mem: 3950 3902 48 9 37 1311
-/+ buffers/cache: 2552 1397
Swap: 255 57 198
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;So I&amp;rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)&lt;/li&gt;
&lt;/ul&gt;
</description> </description>
</item> </item>

View File

@ -136,6 +136,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
&lt;p&gt;&lt;img src=&#34;../images/2016/02/submit-button-ilri.png&#34; alt=&#34;ILRI submission buttons&#34; /&gt; &lt;p&gt;&lt;img src=&#34;../images/2016/02/submit-button-ilri.png&#34; alt=&#34;ILRI submission buttons&#34; /&gt;
&lt;img src=&#34;../images/2016/02/submit-button-drylands.png&#34; alt=&#34;Drylands submission buttons&#34; /&gt;&lt;/p&gt; &lt;img src=&#34;../images/2016/02/submit-button-drylands.png&#34; alt=&#34;Drylands submission buttons&#34; /&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-02-09:124a59adbaa8ef13e1518d003fc03981&#34;&gt;2016-02-09&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Re-sync DSpace Test with CGSpace&lt;/li&gt;
&lt;li&gt;Help Sisay with OpenRefine&lt;/li&gt;
&lt;li&gt;Enable HTTPS on DSpace Test using Let&amp;rsquo;s Encrypt:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;$ 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
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;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: &lt;a href=&#34;https://letsencrypt.org/howitworks/&#34;&gt;https://letsencrypt.org/howitworks/&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;I had to export some CIAT items that were being cleaned up on the test server and I noticed their &lt;code&gt;dc.contributor.author&lt;/code&gt; fields have DSpace 5 authority index UUIDs&amp;hellip;&lt;/li&gt;
&lt;li&gt;To clean those up in OpenRefine I used this GREL expression: &lt;code&gt;value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,&amp;quot;&amp;quot;)&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Getting more and more hangs on DSpace Test, seemingly random but also during CSV import&lt;/li&gt;
&lt;li&gt;Logs don&amp;rsquo;t always show anything right when it fails, but eventually one of these appears:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;or&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Right now DSpace Test&amp;rsquo;s Tomcat heap is set to 1536m and we have quite a bit of free RAM:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;# free -m
total used free shared buffers cached
Mem: 3950 3902 48 9 37 1311
-/+ buffers/cache: 2552 1397
Swap: 255 57 198
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;So I&amp;rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)&lt;/li&gt;
&lt;/ul&gt;
</description> </description>
</item> </item>