From 380ca762af5a5e9cc1f2040c74a0895fa59cde62 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Tue, 9 Feb 2016 18:21:55 +0200 Subject: [PATCH] Add notes for 2016-02-09 Signed-off-by: Alan Orth --- content/2016-02.md | 45 ++++++++++++++++++++++++++++++++ public/2016-02/index.html | 51 +++++++++++++++++++++++++++++++++++++ public/index.xml | 51 +++++++++++++++++++++++++++++++++++++ public/tags/notes/index.xml | 51 +++++++++++++++++++++++++++++++++++++ 4 files changed, 198 insertions(+) diff --git a/content/2016-02.md b/content/2016-02.md index b274c264c..01d4cfeab 100644 --- a/content/2016-02.md +++ b/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) diff --git a/public/2016-02/index.html b/public/2016-02/index.html index 48ee5de70..7f96cc4fb 100644 --- a/public/2016-02/index.html +++ b/public/2016-02/index.html @@ -199,6 +199,57 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start

ILRI submission buttons Drylands submission buttons

+

2016-02-09

+ + + +
$ 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
+
+ + + +
org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
+
+ + + +
Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
+
+ + + +
# free -m
+             total       used       free     shared    buffers     cached
+Mem:          3950       3902         48          9         37       1311
+-/+ buffers/cache:       2552       1397
+Swap:          255         57        198
+
+ + +