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Add notes for 2020-12-01

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Alan Orth 2020-12-01 19:15:48 +02:00
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@ -0,0 +1,24 @@
---
title: "December, 2020"
date: 2020-12-01T11:32:54+02:00
author: "Alan Orth"
categories: ["Notes"]
---
## 2020-12-01
- Atmire responded about the issue with duplicate data in our Solr statistics
- They noticed that some records in the statistics-2015 core haven't been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven't migrated any of the records yet
- That's strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the `cua_version` field
- I started processing those (about 411,000 records):
<!--more-->
```console
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
```
- AReS went down when the `renew-letsencrypt` service stopped the `angular_nginx` container in the pre-update hook and failed to bring it back up
- I ran all system updates on the host and rebooted it and AReS came back up OK
<!-- vim: set sw=2 ts=2: -->

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content/posts/cgspace-dspace6-upgrade.md
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@ -470,7 +470,7 @@ The statistics-2015 core, in 12-hour batches:
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
```
It took ~17 hours to finish processing this core.
It took ~21 hours to finish processing this core.
## statistics-2014

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docs/2015-11/index.html
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@ -239,6 +239,8 @@ db.statementpool = true
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -247,8 +249,6 @@ db.statementpool = true
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2015-12/index.html
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@ -261,6 +261,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -269,8 +271,6 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-01/index.html
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@ -197,6 +197,8 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} ; | sor
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -205,8 +207,6 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} ; | sor
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-02/index.html
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@ -375,6 +375,8 @@ Bitstream: tést señora alimentación.pdf
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -383,8 +385,6 @@ Bitstream: tést señora alimentación.pdf
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-03/index.html
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@ -313,6 +313,8 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -321,8 +323,6 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-04/index.html
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@ -492,6 +492,8 @@ dspace.log.2016-04-27:7271
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -500,8 +502,6 @@ dspace.log.2016-04-27:7271
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-05/index.html
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@ -368,6 +368,8 @@ sys 0m20.540s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -376,8 +378,6 @@ sys 0m20.540s
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-06/index.html
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@ -406,6 +406,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -414,8 +416,6 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-07/index.html
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@ -322,6 +322,8 @@ discovery.index.authority.ignore-variants=true
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -330,8 +332,6 @@ discovery.index.authority.ignore-variants=true
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-08/index.html
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@ -386,6 +386,8 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -394,8 +396,6 @@ $ JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx512m&quot; /home/cgspace.cgiar.org/b
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-09/index.html
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@ -603,6 +603,8 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -611,8 +613,6 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-10/index.html
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@ -369,6 +369,8 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -377,8 +379,6 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-11/index.html
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@ -545,6 +545,8 @@ org.dspace.discovery.SearchServiceException: Error executing query
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -553,8 +555,6 @@ org.dspace.discovery.SearchServiceException: Error executing query
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2016-12/index.html
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@ -781,6 +781,8 @@ $ exit
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -789,8 +791,6 @@ $ exit
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-01/index.html
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@ -366,6 +366,8 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -374,8 +376,6 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-02/index.html
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@ -421,6 +421,8 @@ COPY 1968
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -429,8 +431,6 @@ COPY 1968
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-03/index.html
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@ -352,6 +352,8 @@ $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.spon
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -360,8 +362,6 @@ $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.spon
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-04/index.html
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@ -582,6 +582,8 @@ $ gem install compass -v 1.0.3
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -590,8 +592,6 @@ $ gem install compass -v 1.0.3
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-05/index.html
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@ -388,6 +388,8 @@ UPDATE 187
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -396,8 +398,6 @@ UPDATE 187
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-06/index.html
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@ -267,6 +267,8 @@ $ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace impo
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -275,8 +277,6 @@ $ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace impo
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-07/index.html
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@ -272,6 +272,8 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -280,8 +282,6 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-08/index.html
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@ -514,6 +514,8 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -522,8 +524,6 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-09/index.html
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@ -656,6 +656,8 @@ Cert Status: good
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -664,8 +666,6 @@ Cert Status: good
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-10/index.html
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@ -440,6 +440,8 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -448,8 +450,6 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-11/index.html
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@ -941,6 +941,8 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -949,8 +951,6 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2017-12/index.html
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@ -780,6 +780,8 @@ DELETE 20
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -788,8 +790,6 @@ DELETE 20
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-01/index.html
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@ -1449,6 +1449,8 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1457,8 +1459,6 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-02/index.html
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@ -1036,6 +1036,8 @@ UPDATE 3
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1044,8 +1046,6 @@ UPDATE 3
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-03/index.html
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@ -582,6 +582,8 @@ Fixed 5 occurences of: GENEBANKS
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -590,8 +592,6 @@ Fixed 5 occurences of: GENEBANKS
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-04/index.html
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@ -591,6 +591,8 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -599,8 +601,6 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-05/index.html
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@ -520,6 +520,8 @@ $ psql -h localhost -U postgres dspacetest
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -528,8 +530,6 @@ $ psql -h localhost -U postgres dspacetest
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-06/index.html
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@ -514,6 +514,8 @@ $ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 &gt; map-to-cifor-archive.csv
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -522,8 +524,6 @@ $ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 &gt; map-to-cifor-archive.csv
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-07/index.html
View File

@ -566,6 +566,8 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -574,8 +576,6 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-08/index.html
View File

@ -439,6 +439,8 @@ $ dspace database migrate ignored
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -447,8 +449,6 @@ $ dspace database migrate ignored
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-09/index.html
View File

@ -745,6 +745,8 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -753,8 +755,6 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-10/index.html
View File

@ -653,6 +653,8 @@ $ curl -X GET -H &quot;Content-Type: application/json&quot; -H &quot;Accept: app
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -661,8 +663,6 @@ $ curl -X GET -H &quot;Content-Type: application/json&quot; -H &quot;Accept: app
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-11/index.html
View File

@ -550,6 +550,8 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -558,8 +560,6 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2018-12/index.html
View File

@ -591,6 +591,8 @@ UPDATE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -599,8 +601,6 @@ UPDATE 1
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-01/index.html
View File

@ -1261,6 +1261,8 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1269,8 +1271,6 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-02/index.html
View File

@ -1341,6 +1341,8 @@ Please see the DSpace documentation for assistance.
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1349,8 +1351,6 @@ Please see the DSpace documentation for assistance.
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-03/index.html
View File

@ -1205,6 +1205,8 @@ sys 0m2.551s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1213,8 +1215,6 @@ sys 0m2.551s
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-04/index.html
View File

@ -1296,6 +1296,8 @@ UPDATE 14
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1304,8 +1306,6 @@ UPDATE 14
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-05/index.html
View File

@ -628,6 +628,8 @@ COPY 64871
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -636,8 +638,6 @@ COPY 64871
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-06/index.html
View File

@ -314,6 +314,8 @@ UPDATE 2
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -322,8 +324,6 @@ UPDATE 2
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-07/index.html
View File

@ -551,6 +551,8 @@ issn.validate('1020-3362')
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -559,8 +561,6 @@ issn.validate('1020-3362')
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-08/index.html
View File

@ -570,6 +570,8 @@ sys 2m27.496s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -578,8 +580,6 @@ sys 2m27.496s
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-09/index.html
View File

@ -578,6 +578,8 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -586,8 +588,6 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-10/index.html
View File

@ -382,6 +382,8 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -390,8 +392,6 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-11/index.html
View File

@ -689,6 +689,8 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -697,8 +699,6 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2019-12/index.html
View File

@ -401,6 +401,8 @@ UPDATE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -409,8 +411,6 @@ UPDATE 1
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-01/index.html
View File

@ -601,6 +601,8 @@ COPY 2900
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -609,8 +611,6 @@ COPY 2900
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-02/index.html
View File

@ -1272,6 +1272,8 @@ Moving: 21993 into core statistics-2019
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1280,8 +1282,6 @@ Moving: 21993 into core statistics-2019
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-03/index.html
View File

@ -481,6 +481,8 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -489,8 +491,6 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-04/index.html
View File

@ -655,6 +655,8 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -663,8 +665,6 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-05/index.html
View File

@ -474,6 +474,8 @@ Caused by: java.lang.NullPointerException
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -482,8 +484,6 @@ Caused by: java.lang.NullPointerException
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-06/index.html
View File

@ -808,6 +808,8 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -816,8 +818,6 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-07/index.html
View File

@ -1139,6 +1139,8 @@ Fixed 4 occurences of: Muloi, D.M.
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1147,8 +1149,6 @@ Fixed 4 occurences of: Muloi, D.M.
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-08/index.html
View File

@ -795,6 +795,8 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -803,8 +805,6 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-09/index.html
View File

@ -714,6 +714,8 @@ solr_query_params = {
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -722,8 +724,6 @@ solr_query_params = {
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/2020-10/index.html
View File

@ -1238,6 +1238,8 @@ $ ./delete-metadata-values.py -i 2020-10-31-delete-74-sponsors.csv -db dspace -u
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -1246,8 +1248,6 @@ $ ./delete-metadata-values.py -i 2020-10-31-delete-74-sponsors.csv -db dspace -u
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

8
docs/2020-11/index.html
View File

@ -17,7 +17,7 @@ So far we&rsquo;ve spent at least fifty hours to process the statistics and stat
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-11/" />
<meta property="article:published_time" content="2020-11-01T13:11:54+02:00" />
<meta property="article:modified_time" content="2020-11-29T14:50:02+02:00" />
<meta property="article:modified_time" content="2020-11-30T20:12:55+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="November, 2020"/>
@ -41,7 +41,7 @@ So far we&rsquo;ve spent at least fifty hours to process the statistics and stat
"url": "https://alanorth.github.io/cgspace-notes/2020-11/",
"wordCount": "3655",
"datePublished": "2020-11-01T13:11:54+02:00",
"dateModified": "2020-11-29T14:50:02+02:00",
"dateModified": "2020-11-30T20:12:55+02:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -728,6 +728,8 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -736,8 +738,6 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

212
docs/2020-12/index.html Normal file
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@ -0,0 +1,212 @@
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<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="December, 2020" />
<meta property="og:description" content="2020-12-01
Atmire responded about the issue with duplicate data in our Solr statistics
They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet
That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the cua_version field
I started processing those (about 411,000 records):
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-12/" />
<meta property="article:published_time" content="2020-12-01T11:32:54+02:00" />
<meta property="article:modified_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="December, 2020"/>
<meta name="twitter:description" content="2020-12-01
Atmire responded about the issue with duplicate data in our Solr statistics
They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet
That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the cua_version field
I started processing those (about 411,000 records):
"/>
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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/2020-12/">December, 2020</a></h2>
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<time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-12-01">2020-12-01</h2>
<ul>
<li>Atmire responded about the issue with duplicate data in our Solr statistics
<ul>
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
<li>I started processing those (about 411,000 records):</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
</code></pre><ul>
<li>AReS went down when the <code>renew-letsencrypt</code> service stopped the <code>angular_nginx</code> container in the pre-update hook and failed to bring it back up
<ul>
<li>I ran all system updates on the host and rebooted it and AReS came back up OK</li>
</ul>
</li>
</ul>
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<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
<li><a href="/cgspace-notes/2020-10/">October, 2020</a></li>
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@ -100,8 +102,6 @@
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/categories/notes/">Notes</a></h2>
<p class="blog-post-meta"><time datetime="2020-11-15T13:27:35+02:00">Sun Nov 15, 2020</time> by Alan Orth</p>
<p class="blog-post-meta"><time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time> by Alan Orth</p>
</header>
<a href='https://alanorth.github.io/cgspace-notes/categories/notes/'>Read more →</a>
@ -105,6 +105,8 @@
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<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -113,8 +115,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
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4
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@ -6,11 +6,11 @@
<description>Recent content in Categories on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
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<item>
<title>Notes</title>
<link>https://alanorth.github.io/cgspace-notes/categories/notes/</link>
<pubDate>Sun, 15 Nov 2020 13:27:35 +0200</pubDate>
<pubDate>Tue, 01 Dec 2020 11:32:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/categories/notes/</guid>
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@ -9,7 +9,7 @@
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@ -78,6 +78,33 @@
<article class="blog-post">
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-12/">December, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-12-01">2020-12-01</h2>
<ul>
<li>Atmire responded about the issue with duplicate data in our Solr statistics
<ul>
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
<li>I started processing those (about 411,000 records):</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-12/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></h2>
@ -327,36 +354,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -381,6 +378,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -389,8 +388,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

20
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@ -6,7 +6,25 @@
<description>Recent content in Notes on CGSpace Notes</description>
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<title>December, 2020</title>
<link>https://alanorth.github.io/cgspace-notes/2020-12/</link>
<pubDate>Tue, 01 Dec 2020 11:32:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2020-12/</guid>
<description>&lt;h2 id=&#34;2020-12-01&#34;&gt;2020-12-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Atmire responded about the issue with duplicate data in our Solr statistics
&lt;ul&gt;
&lt;li&gt;They noticed that some records in the statistics-2015 core haven&amp;rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&amp;rsquo;t migrated any of the records yet&lt;/li&gt;
&lt;li&gt;That&amp;rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the &lt;code&gt;cua_version&lt;/code&gt; field&lt;/li&gt;
&lt;li&gt;I started processing those (about 411,000 records):&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>CGSpace DSpace 6 Upgrade</title>
<link>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</link>

62
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@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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@ -78,6 +78,36 @@
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
@ -356,32 +386,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/" rel="prev" role="button">Previous page</a>
@ -406,6 +410,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -414,8 +420,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

64
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@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
@ -78,6 +78,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-05/">May, 2019</a></h2>
@ -362,38 +388,6 @@ sys 0m1.979s
<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>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<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&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;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>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/2/" rel="prev" role="button">Previous page</a>
@ -418,6 +412,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -426,8 +422,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

64
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@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-11-29T14:50:02+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
@ -78,6 +78,38 @@
<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>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<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&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;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>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
@ -378,32 +410,6 @@ COPY 54701
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>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</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/3/" rel="prev" role="button">Previous page</a>
@ -428,6 +434,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -436,8 +444,6 @@ COPY 54701
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

32
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View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2020-11-29T14:50:02+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
@ -78,6 +78,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>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</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
@ -121,6 +147,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -129,8 +157,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/cgiar-library-migration/index.html
View File

@ -279,6 +279,8 @@ dspace=# select setval('handle_seq',86873);
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -287,8 +289,6 @@ dspace=# select setval('handle_seq',86873);
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
docs/cgspace-cgcorev2-migration/index.html
View File

@ -451,6 +451,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -459,8 +461,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

6
docs/cgspace-dspace6-upgrade/index.html
View File

@ -427,7 +427,7 @@ $ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
<h2 id="statistics-2015-1">statistics-2015</h2>
<p>The statistics-2015 core, in 12-hour batches:</p>
<pre><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2015
</code></pre><p>It took ~17 hours to finish processing this core.</p>
</code></pre><p>It took ~21 hours to finish processing this core.</p>
<h2 id="statistics-2014-1">statistics-2014</h2>
<p>The statistics-2014 core, in 12-hour batches:</p>
<pre><code>$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics-2014
@ -468,6 +468,8 @@ $ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -476,8 +478,6 @@ $ chrt -b 0 dspace solr-upgrade-statistics-6x -n 2500000 -i statistics-2018
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

65
docs/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-12/">December, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-12-01">2020-12-01</h2>
<ul>
<li>Atmire responded about the issue with duplicate data in our Solr statistics
<ul>
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
<li>I started processing those (about 411,000 records):</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-12/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></h2>
@ -342,36 +369,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -396,6 +393,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -404,8 +403,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

20
docs/index.xml
View File

@ -6,7 +6,25 @@
<description>Recent content on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Sun, 15 Nov 2020 13:27:35 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="self" type="application/rss+xml" />
<lastBuildDate>Tue, 01 Dec 2020 11:32:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>December, 2020</title>
<link>https://alanorth.github.io/cgspace-notes/2020-12/</link>
<pubDate>Tue, 01 Dec 2020 11:32:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2020-12/</guid>
<description>&lt;h2 id=&#34;2020-12-01&#34;&gt;2020-12-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Atmire responded about the issue with duplicate data in our Solr statistics
&lt;ul&gt;
&lt;li&gt;They noticed that some records in the statistics-2015 core haven&amp;rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&amp;rsquo;t migrated any of the records yet&lt;/li&gt;
&lt;li&gt;That&amp;rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the &lt;code&gt;cua_version&lt;/code&gt; field&lt;/li&gt;
&lt;li&gt;I started processing those (about 411,000 records):&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>CGSpace DSpace 6 Upgrade</title>
<link>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</link>

64
docs/page/2/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,36 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
@ -371,32 +401,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/" rel="prev" role="button">Previous page</a>
@ -421,6 +425,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -429,8 +435,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

66
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View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-05/">May, 2019</a></h2>
@ -377,38 +403,6 @@ sys 0m1.979s
<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>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<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&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;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>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/2/" rel="prev" role="button">Previous page</a>
@ -433,6 +427,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -441,8 +437,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

66
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@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,38 @@
<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>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<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&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;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>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
@ -393,32 +425,6 @@ COPY 54701
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>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</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/3/" rel="prev" role="button">Previous page</a>
@ -443,6 +449,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -451,8 +459,6 @@ COPY 54701
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

57
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View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>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</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
@ -338,29 +364,6 @@ DELETE 1
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/4/" rel="prev" role="button">Previous page</a>
@ -385,6 +388,8 @@ DELETE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -393,8 +398,6 @@ DELETE 1
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

54
docs/page/6/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,29 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
@ -340,29 +363,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00+03:00">Wed Mar 02, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> 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</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-03/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/5/" rel="prev" role="button">Previous page</a>
@ -387,6 +387,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -395,8 +397,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

31
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@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,29 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00+03:00">Wed Mar 02, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> 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</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-02/">February, 2016</a></h2>
@ -220,6 +243,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -228,8 +253,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

65
docs/posts/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,33 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-12/">December, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-12-01">2020-12-01</h2>
<ul>
<li>Atmire responded about the issue with duplicate data in our Solr statistics
<ul>
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
<li>I started processing those (about 411,000 records):</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-12/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></h2>
@ -342,36 +369,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -396,6 +393,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -404,8 +403,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

20
docs/posts/index.xml
View File

@ -6,7 +6,25 @@
<description>Recent content in Posts on CGSpace Notes</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Sun, 15 Nov 2020 13:27:35 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="self" type="application/rss+xml" />
<lastBuildDate>Tue, 01 Dec 2020 11:32:54 +0200</lastBuildDate><atom:link href="https://alanorth.github.io/cgspace-notes/posts/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>December, 2020</title>
<link>https://alanorth.github.io/cgspace-notes/2020-12/</link>
<pubDate>Tue, 01 Dec 2020 11:32:54 +0200</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2020-12/</guid>
<description>&lt;h2 id=&#34;2020-12-01&#34;&gt;2020-12-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Atmire responded about the issue with duplicate data in our Solr statistics
&lt;ul&gt;
&lt;li&gt;They noticed that some records in the statistics-2015 core haven&amp;rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&amp;rsquo;t migrated any of the records yet&lt;/li&gt;
&lt;li&gt;That&amp;rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the &lt;code&gt;cua_version&lt;/code&gt; field&lt;/li&gt;
&lt;li&gt;I started processing those (about 411,000 records):&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;</description>
</item>
<item>
<title>CGSpace DSpace 6 Upgrade</title>
<link>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</link>

64
docs/posts/page/2/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,36 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
@ -371,32 +401,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-06/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/" rel="prev" role="button">Previous page</a>
@ -421,6 +425,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -429,8 +435,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

66
docs/posts/page/3/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-06-02T10:57:51+03:00">Sun Jun 02, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-06/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-05/">May, 2019</a></h2>
@ -377,38 +403,6 @@ sys 0m1.979s
<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>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<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&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;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>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/2/" rel="prev" role="button">Previous page</a>
@ -433,6 +427,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -441,8 +437,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

66
docs/posts/page/4/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,38 @@
<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>
<p class="blog-post-meta"><time datetime="2018-08-01T11:52:54+03:00">Wed Aug 01, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-08-01">2018-08-01</h2>
<ul>
<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&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</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&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;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>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-07/">July, 2018</a></h2>
@ -393,32 +425,6 @@ COPY 54701
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>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</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/3/" rel="prev" role="button">Previous page</a>
@ -443,6 +449,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -451,8 +459,6 @@ COPY 54701
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

57
docs/posts/page/5/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>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</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
@ -338,29 +364,6 @@ DELETE 1
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/4/" rel="prev" role="button">Previous page</a>
@ -385,6 +388,8 @@ DELETE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -393,8 +398,6 @@ DELETE 1
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

54
docs/posts/page/6/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,29 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
@ -340,29 +363,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00+03:00">Wed Mar 02, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> 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</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-03/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/posts/page/5/" rel="prev" role="button">Previous page</a>
@ -387,6 +387,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -395,8 +397,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

31
docs/posts/page/7/index.html
View File

@ -9,7 +9,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
<meta property="og:updated_time" content="2020-11-30T12:10:20+02:00" />
<meta property="og:updated_time" content="2020-12-01T11:32:54+02:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
@ -28,7 +28,7 @@
"@type": "Person",
"name": "Alan Orth"
},
"dateModified": "2020-11-15T13:27:35+02:00",
"dateModified": "2020-12-01T11:32:54+02:00",
"keywords": "notes, migration, notes",
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
@ -93,6 +93,29 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-03/">March, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-03-02T16:50:00+03:00">Wed Mar 02, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> 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</li>
<li>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</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-02/">February, 2016</a></h2>
@ -220,6 +243,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -228,8 +253,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

5
docs/robots.txt
View File

@ -2,11 +2,12 @@ User-agent: *
Disallow: /cgspace-notes/categories/
Disallow: /cgspace-notes/cgspace-dspace6-upgrade/
Disallow: /cgspace-notes/
Disallow: /cgspace-notes/tags/migration/
Disallow: /cgspace-notes/2020-12/
Disallow: /cgspace-notes/categories/notes/
Disallow: /cgspace-notes/posts/
Disallow: /cgspace-notes/cgspace-dspace6-upgrade/
Disallow: /cgspace-notes/tags/migration/
Disallow: /cgspace-notes/tags/
Disallow: /cgspace-notes/2020-11/
Disallow: /cgspace-notes/2020-10/

39
docs/sitemap.xml
View File

@ -4,7 +4,27 @@
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<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
<lastmod>2020-11-29T14:50:02+02:00</lastmod>
<lastmod>2020-12-01T11:32:54+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2020-12-01T11:32:54+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/2020-12/</loc>
<lastmod>2020-12-01T11:32:54+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
<lastmod>2020-12-01T11:32:54+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
<lastmod>2020-12-01T11:32:54+02:00</lastmod>
</url>
<url>
@ -12,26 +32,11 @@
<lastmod>2020-11-29T08:40:58+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2020-11-30T12:10:20+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/migration/</loc>
<lastmod>2020-11-29T08:40:58+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
<lastmod>2020-11-29T14:50:02+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
<lastmod>2020-11-30T12:10:20+02:00</lastmod>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2020-11-30T12:10:20+02:00</lastmod>
@ -39,7 +44,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2020-11/</loc>
<lastmod>2020-11-29T14:50:02+02:00</lastmod>
<lastmod>2020-11-30T20:12:55+02:00</lastmod>
</url>
<url>

4
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@ -119,6 +119,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -127,8 +129,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

4
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@ -152,6 +152,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -160,8 +162,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

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@ -382,6 +382,8 @@ DELETE 1
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -390,8 +392,6 @@ DELETE 1
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

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@ -368,6 +368,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -376,8 +378,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>

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@ -177,6 +177,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></li>
<li><a href="/cgspace-notes/2020-11/">November, 2020</a></li>
@ -185,8 +187,6 @@
<li><a href="/cgspace-notes/2020-09/">September, 2020</a></li>
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
</ol>
</section>