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Add notes for 2018-01-18
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@ -876,3 +876,29 @@ $ mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -Denv=localhost -P \!ds
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- Overall the heap space usage in the munin graph seems ok, though I usually increase it by 512MB over the average a few times per year as usage grows
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- But maybe I should increase it by more, like 1024MB, to give a bit more head room
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## 2018-01-18
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- UptimeRobot said CGSpace was down for 1 minute last night
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- I don't see any errors in the nginx or catalina logs, so I guess UptimeRobot just got impatient and closed the request, which caused nginx to send an HTTP 499
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- I realize I never did a full re-index after the SQL author and affiliation updates last week, so I should force one now:
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```
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$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 /home/cgspace.cgiar.org/bin/dspace index-discovery -b
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```
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- Maria from Bioversity asked if I could remove the abstracts from all of their Limited Access items in the [Bioversity Journal Articles](https://cgspace.cgiar.org/handle/10568/35501) collection
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- It's easy enough to do in OpenRefine, but you have to be careful to only get those items that are uploaded into Bioversity's collection, not the ones that are mapped from others!
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- Use this GREL in OpenRefine after isolating all the Limited Access items: `value.startsWith("10568/35501")`
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- UptimeRobot said CGSpace went down AGAIN and both Sisay and Danny immediately logged in and restarted Tomcat without talking to me *or* each other!
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```
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Jan 18 07:01:22 linode18 sudo[10805]: dhmichael : TTY=pts/5 ; PWD=/home/dhmichael ; USER=root ; COMMAND=/bin/systemctl restart tomcat7
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Jan 18 07:01:22 linode18 sudo[10805]: pam_unix(sudo:session): session opened for user root by dhmichael(uid=0)
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Jan 18 07:01:22 linode18 systemd[1]: Stopping LSB: Start Tomcat....
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Jan 18 07:01:22 linode18 sudo[10812]: swebshet : TTY=pts/3 ; PWD=/home/swebshet ; USER=root ; COMMAND=/bin/systemctl restart tomcat7
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Jan 18 07:01:22 linode18 sudo[10812]: pam_unix(sudo:session): session opened for user root by swebshet(uid=0)
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```
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- For now I've increased the Tomcat JVM heap from 5632 to 6144m, to give ~1GB of free memory over the average usage to hopefully account for spikes caused by load or background jobs
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@ -92,7 +92,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
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<meta property="article:modified_time" content="2018-01-17T18:25:47+02:00"/>
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<meta property="article:modified_time" content="2018-01-17T18:53:01+02:00"/>
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@ -194,9 +194,9 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
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"@type": "BlogPosting",
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"headline": "January, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-01/",
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"wordCount": "4710",
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"wordCount": "4985",
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"datePublished": "2018-01-02T08:35:54-08:00",
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"dateModified": "2018-01-17T18:25:47+02:00",
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"dateModified": "2018-01-17T18:53:01+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -1225,6 +1225,36 @@ $ docker run --network dspace-build --name artifactory -d -v artifactory5_data:/
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<li>But maybe I should increase it by more, like 1024MB, to give a bit more head room</li>
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</ul>
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<h2 id="2018-01-18">2018-01-18</h2>
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<ul>
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<li>UptimeRobot said CGSpace was down for 1 minute last night</li>
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<li>I don’t see any errors in the nginx or catalina logs, so I guess UptimeRobot just got impatient and closed the request, which caused nginx to send an HTTP 499</li>
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<li>I realize I never did a full re-index after the SQL author and affiliation updates last week, so I should force one now:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
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$ time schedtool -D -e ionice -c2 -n7 nice -n19 /home/cgspace.cgiar.org/bin/dspace index-discovery -b
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</code></pre>
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<ul>
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<li>Maria from Bioversity asked if I could remove the abstracts from all of their Limited Access items in the <a href="https://cgspace.cgiar.org/handle/10568/35501">Bioversity Journal Articles</a> collection</li>
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<li>It’s easy enough to do in OpenRefine, but you have to be careful to only get those items that are uploaded into Bioversity’s collection, not the ones that are mapped from others!</li>
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<li>Use this GREL in OpenRefine after isolating all the Limited Access items: <code>value.startsWith("10568/35501")</code></li>
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<li>UptimeRobot said CGSpace went down AGAIN and both Sisay and Danny immediately logged in and restarted Tomcat without talking to me <em>or</em> each other!</li>
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</ul>
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<pre><code>Jan 18 07:01:22 linode18 sudo[10805]: dhmichael : TTY=pts/5 ; PWD=/home/dhmichael ; USER=root ; COMMAND=/bin/systemctl restart tomcat7
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Jan 18 07:01:22 linode18 sudo[10805]: pam_unix(sudo:session): session opened for user root by dhmichael(uid=0)
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Jan 18 07:01:22 linode18 systemd[1]: Stopping LSB: Start Tomcat....
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Jan 18 07:01:22 linode18 sudo[10812]: swebshet : TTY=pts/3 ; PWD=/home/swebshet ; USER=root ; COMMAND=/bin/systemctl restart tomcat7
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Jan 18 07:01:22 linode18 sudo[10812]: pam_unix(sudo:session): session opened for user root by swebshet(uid=0)
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</code></pre>
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<ul>
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<li>For now I’ve increased the Tomcat JVM heap from 5632 to 6144m, to give ~1GB of free memory over the average usage to hopefully account for spikes caused by load or background jobs</li>
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</ul>
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@ -4,7 +4,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/2018-01/</loc>
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<lastmod>2018-01-17T18:25:47+02:00</lastmod>
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<lastmod>2018-01-17T18:53:01+02:00</lastmod>
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</url>
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<url>
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@ -144,7 +144,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2018-01-17T18:25:47+02:00</lastmod>
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<lastmod>2018-01-17T18:53:01+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -155,7 +155,7 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
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<lastmod>2018-01-17T18:25:47+02:00</lastmod>
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<lastmod>2018-01-17T18:53:01+02:00</lastmod>
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<priority>0</priority>
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</url>
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@ -167,13 +167,13 @@
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/post/</loc>
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<lastmod>2018-01-17T18:25:47+02:00</lastmod>
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<lastmod>2018-01-17T18:53:01+02:00</lastmod>
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<priority>0</priority>
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</url>
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
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<lastmod>2018-01-17T18:25:47+02:00</lastmod>
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<lastmod>2018-01-17T18:53:01+02:00</lastmod>
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<priority>0</priority>
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</url>
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