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Add notes for 2020-03-22

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Alan Orth 2020-03-22 14:35:20 +02:00
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5
content/posts/2020-03.md
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@ -264,4 +264,9 @@ $ lein run /tmp/affiliations.csv name id
- Finalized migration of DSpace Test to linode26 and removed linode19
## 2020-03-22
- Look over the AReS ToRs sent by Enrico and Moayad and add a few notes about missing GitHub issues
- Hopefully now they can start working on the development!
<!-- vim: set sw=2 ts=2: -->

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docs/2015-11/index.html
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@ -31,7 +31,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now
$ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspace
78
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docs/2015-12/index.html
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@ -33,7 +33,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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docs/2016-01/index.html
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@ -25,7 +25,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_
I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.
Update GitHub wiki for documentation of maintenance tasks.
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docs/2016-02/index.html
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@ -35,7 +35,7 @@ I noticed we have a very interesting list of countries on CGSpace:
Not only are there 49,000 countries, we have some blanks (25)&hellip;
Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
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docs/2016-03/index.html
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@ -25,7 +25,7 @@ Looking at issues with author authorities on CGSpace
For some reason we still have the index-lucene-update cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module
Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
"/>
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docs/2016-04/index.html
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@ -29,7 +29,7 @@ After running DSpace for over five years I&rsquo;ve never needed to look in any
This will save us a few gigs of backup space we&rsquo;re paying for on S3
Also, I noticed the checker log has some errors we should pay attention to:
"/>
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docs/2016-05/index.html
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@ -31,7 +31,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
# awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
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docs/2016-06/index.html
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@ -31,7 +31,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec
You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
"/>
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docs/2016-07/index.html
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@ -41,7 +41,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
In this case the select query was showing 95 results before the update
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2
docs/2016-08/index.html
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@ -39,7 +39,7 @@ $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
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docs/2016-09/index.html
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@ -31,7 +31,7 @@ It looks like we might be able to use OUs now, instead of DCs:
$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
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docs/2016-10/index.html
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@ -39,7 +39,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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docs/2016-11/index.html
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@ -23,7 +23,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
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docs/2016-12/index.html
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@ -43,7 +43,7 @@ I see thousands of them in the logs for the last few months, so it&rsquo;s not r
I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
"/>
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2
docs/2017-01/index.html
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@ -25,7 +25,7 @@ I checked to see if the Solr sharding task that is supposed to run on January 1s
I tested on DSpace Test as well and it doesn&rsquo;t work there either
I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years
"/>
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docs/2017-02/index.html
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@ -47,7 +47,7 @@ DELETE 1
Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
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docs/2017-03/index.html
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@ -51,7 +51,7 @@ Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing reg
$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600&#43;0&#43;0 8-bit CMYK 168KB 0.000u 0:00.000
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2
docs/2017-04/index.html
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@ -37,7 +37,7 @@ Testing the CMYK patch on a collection with 650 items:
$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
"/>
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2
docs/2017-05/index.html
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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docs/2017-06/index.html
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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docs/2017-07/index.html
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@ -33,7 +33,7 @@ Merge changes for WLE Phase II theme rename (#329)
Looking at extracting the metadata registries from ICARDA&rsquo;s MEL DSpace database so we can compare fields with CGSpace
We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the output into quasi XML:
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2
docs/2017-08/index.html
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@ -57,7 +57,7 @@ This was due to newline characters in the dc.description.abstract column, which
I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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2
docs/2017-09/index.html
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@ -29,7 +29,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two
Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account is both in the approvers step as well as the group
"/>
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2
docs/2017-10/index.html
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@ -31,7 +31,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
"/>
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2
docs/2017-11/index.html
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@ -45,7 +45,7 @@ Generate list of authors on CGSpace for Peter to go through and correct:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
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docs/2017-12/index.html
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@ -27,7 +27,7 @@ The logs say &ldquo;Timeout waiting for idle object&rdquo;
PostgreSQL activity says there are 115 connections currently
The list of connections to XMLUI and REST API for today:
"/>
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2
docs/2018-01/index.html
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@ -147,7 +147,7 @@ dspace.log.2018-01-02:34
Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains
"/>
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docs/2018-02/index.html
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@ -27,7 +27,7 @@ We don&rsquo;t need to distinguish between internal and external works, so that
Yesterday I figured out how to monitor DSpace sessions using JMX
I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
"/>
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docs/2018-03/index.html
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@ -21,7 +21,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
Export a CSV of the IITA community metadata for Martin Mueller
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docs/2018-04/index.html
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@ -23,7 +23,7 @@ Catalina logs at least show some memory errors yesterday:
I tried to test something on DSpace Test but noticed that it&rsquo;s down since god knows when
Catalina logs at least show some memory errors yesterday:
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docs/2018-05/index.html
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@ -35,7 +35,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
Then I reduced the JVM heap size from 6144 back to 5120m
Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use
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docs/2018-06/index.html
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@ -55,7 +55,7 @@ real 74m42.646s
user 8m5.056s
sys 2m7.289s
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docs/2018-07/index.html
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@ -33,7 +33,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r
There is insufficient memory for the Java Runtime Environment to continue.
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docs/2018-08/index.html
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@ -43,7 +43,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did
The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes
I ran all system updates on DSpace Test and rebooted it
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docs/2018-09/index.html
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@ -27,7 +27,7 @@ I&rsquo;ll update the DSpace role in our Ansible infrastructure playbooks and ru
Also, I&rsquo;ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month
I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:
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docs/2018-10/index.html
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@ -23,7 +23,7 @@ I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nai
Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items
I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nairobi right now
"/>
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docs/2018-11/index.html
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@ -33,7 +33,7 @@ Send a note about my dspace-statistics-api to the dspace-tech mailing list
Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
Today these are the top 10 IPs:
"/>
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docs/2018-12/index.html
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@ -33,7 +33,7 @@ Then I ran all system updates and restarted the server
I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week
"/>
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docs/2019-01/index.html
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@ -47,7 +47,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
357 207.46.13.1
903 54.70.40.11
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docs/2019-02/index.html
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@ -69,7 +69,7 @@ real 0m19.873s
user 0m22.203s
sys 0m1.979s
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docs/2019-03/index.html
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@ -43,7 +43,7 @@ Most worryingly, there are encoding errors in the abstracts for eleven items, fo
I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs
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@ -639,9 +639,9 @@ Max realtime timeout unlimited unlimited us
<li>I sent a mail to the dspace-tech mailing list to ask about Solr issues</li>
<li>Testing Solr 4.10.4 on DSpace 5.8:
<ul>
<li><input checked="" disabled="" type="checkbox">Discovery indexing</li>
<li><input checked="" disabled="" type="checkbox">dspace-statistics-api indexer</li>
<li><input checked="" disabled="" type="checkbox">/solr admin UI</li>
<li><input checked="" disabled="" type="checkbox"> Discovery indexing</li>
<li><input checked="" disabled="" type="checkbox"> dspace-statistics-api indexer</li>
<li><input checked="" disabled="" type="checkbox"> /solr admin UI</li>
</ul>
</li>
</ul>

2
docs/2019-04/index.html
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@ -61,7 +61,7 @@ $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u ds
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
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docs/2019-05/index.html
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@ -45,7 +45,7 @@ DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present&hellip;
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docs/2019-06/index.html
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@ -31,7 +31,7 @@ Run system updates on CGSpace (linode18) and reboot it
Skype with Marie-Angélique and Abenet about CG Core v2
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docs/2019-07/index.html
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@ -35,7 +35,7 @@ CGSpace
Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
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docs/2019-08/index.html
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@ -43,7 +43,7 @@ After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s luck
Run system updates on DSpace Test (linode19) and reboot it
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docs/2019-09/index.html
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@ -69,7 +69,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
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docs/2019-10/index.html
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2019"/>
<meta name="twitter:description" content="2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U&#43;00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c &#39;id,dc."/>
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docs/2019-11/index.html
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@ -55,7 +55,7 @@ Let&rsquo;s see how many of the REST API requests were for bitstreams (because t
# zcat --force /var/log/nginx/rest.log.*.gz | grep -E &quot;[0-9]{1,2}/Oct/2019&quot; | grep -c -E &quot;/rest/bitstreams&quot;
106781
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docs/2019-12/index.html
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@ -43,7 +43,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C
# reboot
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docs/2020-01/index.html
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@ -53,7 +53,7 @@ I tweeted the CGSpace repository link
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@ -35,7 +35,7 @@ The code finally builds and runs with a fresh install
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@ -241,10 +241,10 @@ DROP VIEW
</li>
<li>Issues remaining in the DSpace 6 port of our CGSpace 5.x code:
<ul>
<li><input checked="" disabled="" type="checkbox">Community and collection pages only show one recent submission (seems that there is only one item in Solr?)</li>
<li><input checked="" disabled="" type="checkbox">Community and collection pages have tons of &ldquo;Browse&rdquo; buttons that we need to remove</li>
<li><input checked="" disabled="" type="checkbox">Order of navigation elements in right side bar (&ldquo;My Account&rdquo; etc, compare to DSpace Test)</li>
<li><input disabled="" type="checkbox">Home page trail says &ldquo;CGSpace Home&rdquo; instead of &ldquo;CGSpace Home / Community List&rdquo; (see DSpace Test)</li>
<li><input checked="" disabled="" type="checkbox"> Community and collection pages only show one recent submission (seems that there is only one item in Solr?)</li>
<li><input checked="" disabled="" type="checkbox"> Community and collection pages have tons of &ldquo;Browse&rdquo; buttons that we need to remove</li>
<li><input checked="" disabled="" type="checkbox"> Order of navigation elements in right side bar (&ldquo;My Account&rdquo; etc, compare to DSpace Test)</li>
<li><input disabled="" type="checkbox"> Home page trail says &ldquo;CGSpace Home&rdquo; instead of &ldquo;CGSpace Home / Community List&rdquo; (see DSpace Test)</li>
</ul>
</li>
<li>There are lots of errors in the DSpace log, which might explain some of the issues with recent submissions / Solr:</li>

12
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@ -39,7 +39,7 @@ You need to download this into the DSpace 6.x source and compile it
"/>
<meta name="generator" content="Hugo 0.67.1" />
<meta name="generator" content="Hugo 0.68.0" />
@ -49,7 +49,7 @@ You need to download this into the DSpace 6.x source and compile it
"@type": "BlogPosting",
"headline": "March, 2020",
"url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-03\/",
"wordCount": "1546",
"wordCount": "1575",
"datePublished": "2020-03-02T12:31:30+02:00",
"dateModified": "2020-03-19T12:19:11+02:00",
"author": {
@ -391,6 +391,14 @@ $ lein run /tmp/affiliations.csv name id
<ul>
<li>Finalized migration of DSpace Test to linode26 and removed linode19</li>
</ul>
<h2 id="2020-03-22">2020-03-22</h2>
<ul>
<li>Look over the AReS ToRs sent by Enrico and Moayad and add a few notes about missing GitHub issues
<ul>
<li>Hopefully now they can start working on the development!</li>
</ul>
</li>
</ul>
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGIAR Library Migration"/>
<meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
<meta name="generator" content="Hugo 0.67.1" />
<meta name="generator" content="Hugo 0.68.0" />
@ -108,26 +108,26 @@
<h2 id="pre-migration-technical-todos">Pre-migration Technical TODOs</h2>
<p>Things that need to happen before the migration:</p>
<ul>
<li><input checked="" disabled="" type="checkbox">Create top-level community on CGSpace to hold the CGIAR Library content: <code>10568/83389</code>
<li><input checked="" disabled="" type="checkbox"> Create top-level community on CGSpace to hold the CGIAR Library content: <code>10568/83389</code>
<ul>
<li><input checked="" disabled="" type="checkbox">Update nginx redirects in ansible templates</li>
<li><input checked="" disabled="" type="checkbox">Update handle in DSpace XMLUI config</li>
<li><input checked="" disabled="" type="checkbox"> Update nginx redirects in ansible templates</li>
<li><input checked="" disabled="" type="checkbox"> Update handle in DSpace XMLUI config</li>
</ul>
</li>
<li>Set up nginx redirects for URLs like:
<ul>
<li><input checked="" disabled="" type="checkbox"><a href="https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf">https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf</a></li>
<li><input checked="" disabled="" type="checkbox"><a href="https://library.cgiar.org/handle/10947/4258">https://library.cgiar.org/handle/10947/4258</a></li>
<li><input checked="" disabled="" type="checkbox"> <a href="https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf">https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf</a></li>
<li><input checked="" disabled="" type="checkbox"> <a href="https://library.cgiar.org/handle/10947/4258">https://library.cgiar.org/handle/10947/4258</a></li>
</ul>
</li>
<li><input checked="" disabled="" type="checkbox">Merge <a href="https://github.com/ilri/DSpace/pull/339">#339</a> to <code>5_x-prod</code> branch and rebuild DSpace</li>
<li><input checked="" disabled="" type="checkbox">Increase <code>max_connections</code> in <code>/etc/postgresql/9.5/main/postgresql.conf</code> by ~10
<li><input checked="" disabled="" type="checkbox"> Merge <a href="https://github.com/ilri/DSpace/pull/339">#339</a> to <code>5_x-prod</code> branch and rebuild DSpace</li>
<li><input checked="" disabled="" type="checkbox"> Increase <code>max_connections</code> in <code>/etc/postgresql/9.5/main/postgresql.conf</code> by ~10
<ul>
<li><code>SELECT * FROM pg_stat_activity;</code> seems to show ~6 extra connections used by the command line tools during import</li>
</ul>
</li>
<li><input checked="" disabled="" type="checkbox">Temporarily disable nightly <code>index-discovery</code> cron job because the import process will be taking place during some of this time and I don&rsquo;t want them to be competing to update the Solr index</li>
<li><input checked="" disabled="" type="checkbox">Copy HTTPS certificate key pair from CGIAR Library server&rsquo;s Tomcat keystore:</li>
<li><input checked="" disabled="" type="checkbox"> Temporarily disable nightly <code>index-discovery</code> cron job because the import process will be taking place during some of this time and I don&rsquo;t want them to be competing to update the Solr index</li>
<li><input checked="" disabled="" type="checkbox"> Copy HTTPS certificate key pair from CGIAR Library server&rsquo;s Tomcat keystore:</li>
</ul>
<pre><code>$ keytool -list -keystore tomcat.keystore
$ keytool -importkeystore -srckeystore tomcat.keystore -destkeystore library.cgiar.org.p12 -deststoretype PKCS12 -srcalias tomcat
@ -152,13 +152,13 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93760 10568-93760/105
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
</code></pre><p><strong>Import to CGSpace (also see <a href="http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10">notes from 2017-05-10</a>):</strong></p>
<ul>
<li><input checked="" disabled="" type="checkbox">Copy all exports from DSpace Test</li>
<li><input checked="" disabled="" type="checkbox">Add ingestion overrides to <code>dspace.cfg</code> before import:</li>
<li><input checked="" disabled="" type="checkbox"> Copy all exports from DSpace Test</li>
<li><input checked="" disabled="" type="checkbox"> Add ingestion overrides to <code>dspace.cfg</code> before import:</li>
</ul>
<pre><code>mets.dspaceAIP.ingest.crosswalk.METSRIGHTS = NIL
mets.dspaceAIP.ingest.crosswalk.DSPACE-ROLES = NIL
</code></pre><ul>
<li><input checked="" disabled="" type="checkbox">Import communities and collections, paying attention to options to skip missing parents and ignore handles:</li>
<li><input checked="" disabled="" type="checkbox"> Import communities and collections, paying attention to options to skip missing parents and ignore handles:</li>
</ul>
<pre><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit -XX:+TieredCompilation -XX:TieredStopAtLevel=1&quot;
$ export PATH=$PATH:/home/cgspace.cgiar.org/bin
@ -179,9 +179,9 @@ $ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@
</code></pre><p>This submits AIP hierarchies recursively (-r) and suppresses errors when an item&rsquo;s parent collection hasn&rsquo;t been created yet—for example, if the item is mapped. The large historic archive (10947/1) is created in several steps because it requires a lot of memory and often crashes.</p>
<p><strong>Create new subcommunities and collections for content we reorganized into new hierarchies from the original:</strong></p>
<ul>
<li><input checked="" disabled="" type="checkbox">Create <em>CGIAR System Management Board</em> sub-community: <code>10568/83536</code>
<li><input checked="" disabled="" type="checkbox"> Create <em>CGIAR System Management Board</em> sub-community: <code>10568/83536</code>
<ul>
<li><input checked="" disabled="" type="checkbox">Content from <em>CGIAR System Management Board documents</em> collection (<code>10947/4561</code>) goes here</li>
<li><input checked="" disabled="" type="checkbox"> Content from <em>CGIAR System Management Board documents</em> collection (<code>10947/4561</code>) goes here</li>
<li>Import collection hierarchy first and then the items:</li>
</ul>
</li>
@ -189,9 +189,9 @@ $ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@
<pre><code>$ dspace packager -r -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83536 10568-93760/COLLECTION@10947-4651.zip
$ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
</code></pre><ul>
<li><input checked="" disabled="" type="checkbox">Create <em>CGIAR System Management Office</em> sub-community: <code>10568/83537</code>
<li><input checked="" disabled="" type="checkbox"> Create <em>CGIAR System Management Office</em> sub-community: <code>10568/83537</code>
<ul>
<li><input checked="" disabled="" type="checkbox">Create <em>CGIAR System Management Office documents</em> collection: <code>10568/83538</code></li>
<li><input checked="" disabled="" type="checkbox"> Create <em>CGIAR System Management Office documents</em> collection: <code>10568/83538</code></li>
<li>Import items to collection individually in replace mode (-r) while explicitly preserving handles and ignoring parents:</li>
</ul>
</li>
@ -209,11 +209,11 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
<pre><code>$ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done
</code></pre><h2 id="post-migration">Post Migration</h2>
<ul>
<li><input checked="" disabled="" type="checkbox">Shut down Tomcat and run <code>update-sequences.sql</code> as the system&rsquo;s <code>postgres</code> user</li>
<li><input checked="" disabled="" type="checkbox">Remove ingestion overrides from <code>dspace.cfg</code></li>
<li><input checked="" disabled="" type="checkbox">Reset PostgreSQL <code>max_connections</code> to 183</li>
<li><input checked="" disabled="" type="checkbox">Enable nightly <code>index-discovery</code> cron job</li>
<li><input checked="" disabled="" type="checkbox">Adjust CGSpace&rsquo;s <code>handle-server/config.dct</code> to add the new prefix alongside our existing 10568, ie:</li>
<li><input checked="" disabled="" type="checkbox"> Shut down Tomcat and run <code>update-sequences.sql</code> as the system&rsquo;s <code>postgres</code> user</li>
<li><input checked="" disabled="" type="checkbox"> Remove ingestion overrides from <code>dspace.cfg</code></li>
<li><input checked="" disabled="" type="checkbox"> Reset PostgreSQL <code>max_connections</code> to 183</li>
<li><input checked="" disabled="" type="checkbox"> Enable nightly <code>index-discovery</code> cron job</li>
<li><input checked="" disabled="" type="checkbox"> Adjust CGSpace&rsquo;s <code>handle-server/config.dct</code> to add the new prefix alongside our existing 10568, ie:</li>
</ul>
<pre><code>&quot;server_admins&quot; = (
&quot;300:0.NA/10568&quot;
@ -231,15 +231,15 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
)
</code></pre><p>I had been regenerated the <code>sitebndl.zip</code> file on the CGIAR Library server and sent it to the Handle.net admins but they said that there were mismatches between the public and private keys, which I suspect is due to <code>make-handle-config</code> not being very flexible. After discussing our scenario with the Handle.net admins they said we actually don&rsquo;t need to send an updated <code>sitebndl.zip</code> for this type of change, and the above <code>config.dct</code> edits are all that is required. I guess they just did something on their end by setting the authoritative IP address for the 10947 prefix to be the same as ours&hellip;</p>
<ul>
<li><input checked="" disabled="" type="checkbox">Update DNS records:
<li><input checked="" disabled="" type="checkbox"> Update DNS records:
<ul>
<li>CNAME: cgspace.cgiar.org</li>
</ul>
</li>
<li><input checked="" disabled="" type="checkbox">Re-deploy DSpace from freshly built <code>5_x-prod</code> branch</li>
<li><input checked="" disabled="" type="checkbox">Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</li>
<li><input checked="" disabled="" type="checkbox">Run system updates and reboot server</li>
<li><input checked="" disabled="" type="checkbox">Switch to Let&rsquo;s Encrypt HTTPS certificates (after DNS is updated and server isn&rsquo;t busy):</li>
<li><input checked="" disabled="" type="checkbox"> Re-deploy DSpace from freshly built <code>5_x-prod</code> branch</li>
<li><input checked="" disabled="" type="checkbox"> Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</li>
<li><input checked="" disabled="" type="checkbox"> Run system updates and reboot server</li>
<li><input checked="" disabled="" type="checkbox"> Switch to Let&rsquo;s Encrypt HTTPS certificates (after DNS is updated and server isn&rsquo;t busy):</li>
</ul>
<pre><code>$ sudo systemctl stop nginx
$ /opt/certbot-auto certonly --standalone -d library.cgiar.org

26
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace CG Core v2 Migration"/>
<meta name="twitter:description" content="Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2."/>
<meta name="generator" content="Hugo 0.67.1" />
<meta name="generator" content="Hugo 0.68.0" />
@ -176,22 +176,22 @@
<h2 id="fields-to-create">Fields to Create</h2>
<p>Make sure the following fields exist:</p>
<ul>
<li><input checked="" disabled="" type="checkbox">cg.creator.identifier (242)</li>
<li><input checked="" disabled="" type="checkbox">cg.contributor.donor (243)</li>
<li><input checked="" disabled="" type="checkbox">cg.review-status (244)</li>
<li><input checked="" disabled="" type="checkbox">cg.howpublished (245)</li>
<li><input checked="" disabled="" type="checkbox">cg.journal (246)</li>
<li><input checked="" disabled="" type="checkbox">cg.isbn (247)</li>
<li><input checked="" disabled="" type="checkbox">cg.issn (248)</li>
<li><input checked="" disabled="" type="checkbox"> cg.creator.identifier (242)</li>
<li><input checked="" disabled="" type="checkbox"> cg.contributor.donor (243)</li>
<li><input checked="" disabled="" type="checkbox"> cg.review-status (244)</li>
<li><input checked="" disabled="" type="checkbox"> cg.howpublished (245)</li>
<li><input checked="" disabled="" type="checkbox"> cg.journal (246)</li>
<li><input checked="" disabled="" type="checkbox"> cg.isbn (247)</li>
<li><input checked="" disabled="" type="checkbox"> cg.issn (248)</li>
</ul>
<h2 id="fields-to-delete">Fields to delete</h2>
<p>Fields to delete after migration:</p>
<ul>
<li><input disabled="" type="checkbox">cg.creator.id</li>
<li><input disabled="" type="checkbox">cg.fulltextstatus</li>
<li><input disabled="" type="checkbox">cg.identifier.status</li>
<li><input disabled="" type="checkbox">cg.link.reference</li>
<li><input disabled="" type="checkbox">cg.targetaudience</li>
<li><input disabled="" type="checkbox"> cg.creator.id</li>
<li><input disabled="" type="checkbox"> cg.fulltextstatus</li>
<li><input disabled="" type="checkbox"> cg.identifier.status</li>
<li><input disabled="" type="checkbox"> cg.link.reference</li>
<li><input disabled="" type="checkbox"> cg.targetaudience</li>
</ul>
<h2 id="implementation-progress">Implementation Progress</h2>
<p>Tally of the status of the implementation of the new fields in the CGSpace <code>5_x-cgcorev2</code> branch.</p>

2
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