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2019-10-11 10:19:42 +02:00
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< h1 class = "blog-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< p class = "lead blog-description" dir = "auto" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-11/" > November, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-11-01T16:41:30+02:00" > Thu Nov 01, 2018< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2018-11-01" > 2018-11-01< / h2 >
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< li > Finalize AReS Phase I and Phase II ToRs< / li >
< li > Send a note about my < a href = "https://github.com/ilri/dspace-statistics-api" > dspace-statistics-api< / a > to the dspace-tech mailing list< / li >
< / ul >
< h2 id = "2018-11-03" > 2018-11-03< / h2 >
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< li > Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage< / li >
< li > Today these are the top 10 IPs:< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-11/' > Read more →< / a >
< / article >
2020-05-02 09:08:14 +02:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-10/" > October, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-10-01T22:31:54+03:00" > Mon Oct 01, 2018< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2018-10-01" > 2018-10-01< / h2 >
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< li > Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items< / li >
< li > I created a GitHub issue to track this < a href = "https://github.com/ilri/DSpace/issues/389" > #389< / a > , because I’ m super busy in Nairobi right now< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-10/' > Read more →< / a >
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2020-04-02 09:54:46 +02:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-09/" > September, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-09-02T09:55:54+03:00" > Sun Sep 02, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2018-09-02" > 2018-09-02< / h2 >
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< li > New < a href = "https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5" > PostgreSQL JDBC driver version 42.2.5< / a > < / li >
< li > I’ ll update the DSpace role in our < a href = "https://github.com/ilri/rmg-ansible-public" > Ansible infrastructure playbooks< / a > and run the updated playbooks on CGSpace and DSpace Test< / li >
< li > Also, I’ ll re-run the < code > postgresql< / code > tasks because the custom PostgreSQL variables are dynamic according to the system’ s RAM, and we never re-ran them after migrating to larger Linodes last month< / li >
< li > I’ m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’ m getting those autowire errors in Tomcat 8.5.30 again:< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-09/' > Read more →< / a >
< / article >
2020-03-02 11:38:10 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-08/" > August, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-08-01T11:52:54+03:00" > Wed Aug 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / header >
< h2 id = "2018-08-01" > 2018-08-01< / h2 >
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< li > DSpace Test had crashed at some point yesterday morning and I see the following in < code > dmesg< / code > :< / li >
< / ul >
< pre > < code > [Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
< / code > < / pre > < ul >
< li > Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight< / li >
< li > From the DSpace log I see that eventually Solr stopped responding, so I guess the < code > java< / code > process that was OOM killed above was Tomcat’ s< / li >
< li > I’ m not sure why Tomcat didn’ t crash with an OutOfMemoryError… < / li >
< li > Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core< / li >
< li > The server only has 8GB of RAM so we’ ll eventually need to upgrade to a larger one because we’ ll start starving the OS, PostgreSQL, and command line batch processes< / li >
< li > I ran all system updates on DSpace Test and rebooted it< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-08/' > Read more →< / a >
< / article >
2020-02-02 16:15:48 +01:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-07/" > July, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-07-01T12:56:54+03:00" > Sun Jul 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2018-07-01" > 2018-07-01< / h2 >
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< li > I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:< / li >
< / ul >
< pre > < code > $ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
< / code > < / pre > < ul >
< li > During the < code > mvn package< / code > stage on the 5.8 branch I kept getting issues with java running out of memory:< / li >
< / ul >
< pre > < code > There is insufficient memory for the Java Runtime Environment to continue.
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-07/' > Read more →< / a >
< / article >
2020-01-06 10:14:44 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-06/" > June, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-06-04T19:49:54-07:00" > Mon Jun 04, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
< h2 id = "2018-06-04" > 2018-06-04< / h2 >
< ul >
< li > Test the < a href = "https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560" > DSpace 5.8 module upgrades from Atmire< / a > (< a href = "https://github.com/ilri/DSpace/pull/378" > #378< / a > )
< ul >
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< li > There seems to be a problem with the CUA and L& R versions in < code > pom.xml< / code > because they are using SNAPSHOT and it doesn’ t build< / li >
2020-01-06 10:14:44 +01:00
< / ul >
< / li >
< li > I added the new CCAFS Phase II Project Tag < code > PII-FP1_PACCA2< / code > and merged it into the < code > 5_x-prod< / code > branch (< a href = "https://github.com/ilri/DSpace/pull/379" > #379< / a > )< / li >
< li > I proofed and tested the ILRI author corrections that Peter sent back to me this week:< / li >
< / ul >
< pre > < code > $ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
< / code > < / pre > < ul >
< li > I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in < a href = "/cgspace-notes/2018-03/" > March, 2018< / a > < / li >
< li > Time to index ~70,000 items on CGSpace:< / li >
< / ul >
< pre > < code > $ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
real 74m42.646s
user 8m5.056s
sys 2m7.289s
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-06/' > Read more →< / a >
< / article >
2019-12-01 10:29:49 +01:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-05/" > May, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-05-01T16:43:54+03:00" > Tue May 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2018-05-01" > 2018-05-01< / h2 >
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< ul >
< li > I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
< ul >
< li > http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E< / li >
< li > http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E< / li >
< / ul >
< / li >
< li > Then I reduced the JVM heap size from 6144 back to 5120m< / li >
< li > Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the < a href = "https://github.com/ilri/rmg-ansible-public" > Ansible infrastructure scripts< / a > to support hosts choosing which distribution they want to use< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-05/' > Read more →< / a >
< / article >
2019-11-04 15:41:19 +01:00
< article class = "blog-post" >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-04/" > April, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-04-01T16:13:54+02:00" > Sun Apr 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-04-01" > 2018-04-01< / h2 >
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< li > I tried to test something on DSpace Test but noticed that it’ s down since god knows when< / li >
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< li > Catalina logs at least show some memory errors yesterday:< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-04/' > Read more →< / a >
< / article >
2019-10-28 12:43:25 +01:00
< article class = "blog-post" >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-03/" > March, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-03-02T16:07:54+02:00" > Fri Mar 02, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-03-02" > 2018-03-02< / h2 >
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< ul >
< li > Export a CSV of the IITA community metadata for Martin Mueller< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-03/' > Read more →< / a >
< / article >
2019-10-01 16:31:40 +02:00
< article class = "blog-post" >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-02/" > February, 2018< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2018-02-01T16:28:54+02:00" > Thu Feb 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
2019-10-01 16:31:40 +02:00
< / p >
< / header >
2019-12-17 13:49:24 +01:00
< h2 id = "2018-02-01" > 2018-02-01< / h2 >
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< ul >
< li > Peter gave feedback on the < code > dc.rights< / code > proof of concept that I had sent him last week< / li >
2020-01-27 15:20:44 +01:00
< li > We don’ t need to distinguish between internal and external works, so that makes it just a simple list< / li >
2019-10-01 16:31:40 +02:00
< li > Yesterday I figured out how to monitor DSpace sessions using JMX< / li >
2020-01-27 15:20:44 +01:00
< li > I copied the logic in the < code > jmx_tomcat_dbpools< / code > provided by Ubuntu’ s < code > munin-plugins-java< / code > package and used the stuff I discovered about JMX < a href = "/cgspace-notes/2018-01/" > in 2018-01< / a > < / li >
2019-10-01 16:31:40 +02:00
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< a href = 'https://alanorth.github.io/cgspace-notes/2018-02/' > Read more →< / a >
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2018-02-11 17:28:23 +01:00
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< h4 > Recent Posts< / h4 >
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< li > < a href = "/cgspace-notes/2020-06/" > June, 2020< / a > < / li >
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< li > < a href = "/cgspace-notes/2020-05/" > May, 2020< / a > < / li >
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< li > < a href = "/cgspace-notes/2020-04/" > April, 2020< / a > < / li >
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< li > < a href = "/cgspace-notes/2020-03/" > March, 2020< / a > < / li >
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< li > < a href = "/cgspace-notes/2020-02/" > February, 2020< / a > < / li >
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< h4 > Links< / h4 >
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< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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