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Add notes for 2018-04-29

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Alan Orth 2018-04-29 12:36:13 +03:00
parent be4df4f64f
commit df0a3f2417
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
54 changed files with 114 additions and 59 deletions
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25
content/posts/2018-04.md
View File

@ -506,3 +506,28 @@ org.apache.tomcat.jdbc.pool.PoolExhaustedException: [localhost-startStop-2] Time
$ psql dspacetest -c 'alter user dspacetest superuser;'
$ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-18.backup
```
- There's another issue with Tomcat in Ubuntu 18.04:
```
25-Apr-2018 13:26:21.493 SEVERE [http-nio-127.0.0.1-8443-exec-1] org.apache.coyote.AbstractProtocol$ConnectionHandler.process Error reading request, ignored
java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;
at org.apache.coyote.http11.Http11InputBuffer.init(Http11InputBuffer.java:688)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:672)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
```
- There's a [Debian bug about this from a few weeks ago](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895866)
- Apparently Tomcat was compiled with Java 9, so doesn't work with Java 8
## 2018-04-29
- DSpace Test crashed again, looks like memory issues again
- JVM heap size was last increased to 6144m but the system only has 8GB total so there's not much we can do here other than get a bigger Linode instance or remove the massive Solr Statistics data

2
docs/2015-11/index.html
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@ -53,7 +53,7 @@ $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspac
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2015-12/index.html
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@ -55,7 +55,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-01/index.html
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@ -45,7 +45,7 @@ Update GitHub wiki for documentation of maintenance tasks.
"/>
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2
docs/2016-02/index.html
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@ -59,7 +59,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-03/index.html
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@ -45,7 +45,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-04/index.html
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@ -49,7 +49,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
"/>
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<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-05/index.html
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@ -53,7 +53,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-06/index.html
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@ -51,7 +51,7 @@ Working on second phase of metadata migration, looks like this will work for mov
"/>
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<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-07/index.html
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@ -67,7 +67,7 @@ In this case the select query was showing 95 results before the update
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-08/index.html
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@ -61,7 +61,7 @@ $ git rebase -i dspace-5.5
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-09/index.html
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@ -53,7 +53,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-10/index.html
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@ -61,7 +61,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-11/index.html
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@ -45,7 +45,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2016-12/index.html
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@ -69,7 +69,7 @@ Another worrying error from dspace.log is:
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-01/index.html
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@ -45,7 +45,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-02/index.html
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@ -73,7 +73,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-03/index.html
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@ -77,7 +77,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-04/index.html
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@ -63,7 +63,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-05/index.html
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@ -29,7 +29,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-06/index.html
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@ -29,7 +29,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-07/index.html
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@ -57,7 +57,7 @@ We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the
"/>
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<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-08/index.html
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@ -77,7 +77,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-09/index.html
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@ -53,7 +53,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-10/index.html
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@ -57,7 +57,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-11/index.html
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@ -77,7 +77,7 @@ COPY 54701
"/>
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<meta name="generator" content="Hugo 0.40.1" />

2
docs/2017-12/index.html
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@ -47,7 +47,7 @@ The list of connections to XMLUI and REST API for today:
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/2018-01/index.html
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@ -185,7 +185,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
"/>
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<meta name="generator" content="Hugo 0.40.1" />

2
docs/2018-02/index.html
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@ -47,7 +47,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
"/>
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<meta name="generator" content="Hugo 0.40.1" />

2
docs/2018-03/index.html
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@ -41,7 +41,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
"/>
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<meta name="generator" content="Hugo 0.40.1" />

36
docs/2018-04/index.html
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@ -21,7 +21,7 @@ Catalina logs at least show some memory errors yesterday:
<meta property="article:published_time" content="2018-04-01T16:13:54&#43;02:00"/>
<meta property="article:modified_time" content="2018-04-24T16:53:28&#43;03:00"/>
<meta property="article:modified_time" content="2018-04-25T13:15:38&#43;03:00"/>
@ -43,7 +43,7 @@ Catalina logs at least show some memory errors yesterday:
"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />
@ -55,7 +55,7 @@ Catalina logs at least show some memory errors yesterday:
"url": "https://alanorth.github.io/cgspace-notes/2018-04/",
"wordCount": "0",
"datePublished": "2018-04-01T16:13:54&#43;02:00",
"dateModified": "2018-04-24T16:53:28&#43;03:00",
"dateModified": "2018-04-25T13:15:38&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -686,6 +686,36 @@ org.apache.tomcat.jdbc.pool.PoolExhaustedException: [localhost-startStop-2] Time
$ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-18.backup
</code></pre>
<ul>
<li>There&rsquo;s another issue with Tomcat in Ubuntu 18.04:</li>
</ul>
<pre><code>25-Apr-2018 13:26:21.493 SEVERE [http-nio-127.0.0.1-8443-exec-1] org.apache.coyote.AbstractProtocol$ConnectionHandler.process Error reading request, ignored
java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;
at org.apache.coyote.http11.Http11InputBuffer.init(Http11InputBuffer.java:688)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:672)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
</code></pre>
<ul>
<li>There&rsquo;s a <a href="https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895866">Debian bug about this from a few weeks ago</a></li>
<li>Apparently Tomcat was compiled with Java 9, so doesn&rsquo;t work with Java 8</li>
</ul>
<h2 id="2018-04-29">2018-04-29</h2>
<ul>
<li>DSpace Test crashed again, looks like memory issues again</li>
<li>JVM heap size was last increased to 6144m but the system only has 8GB total so there&rsquo;s not much we can do here other than get a bigger Linode instance or remove the massive Solr Statistics data</li>
</ul>

2
docs/404.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="404 Page not found"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/categories/index.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/categories/notes/index.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/categories/page/2/index.html
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/categories/page/3/index.html
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/categories/page/4/index.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/cgiar-library-migration/index.html
View File

@ -29,7 +29,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGIAR Library Migration"/>
<meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/page/3/index.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/posts/index.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
docs/posts/page/4/index.html
View File

@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Posts"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

10
docs/sitemap.xml
View File

@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2018-04/</loc>
<lastmod>2018-04-24T16:53:28+03:00</lastmod>
<lastmod>2018-04-25T13:15:38+03:00</lastmod>
</url>
<url>
@ -159,7 +159,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2018-04-24T16:53:28+03:00</lastmod>
<lastmod>2018-04-25T13:15:38+03:00</lastmod>
<priority>0</priority>
</url>
@ -170,7 +170,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2018-04-24T16:53:28+03:00</lastmod>
<lastmod>2018-04-25T13:15:38+03:00</lastmod>
<priority>0</priority>
</url>
@ -182,13 +182,13 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
<lastmod>2018-04-24T16:53:28+03:00</lastmod>
<lastmod>2018-04-25T13:15:38+03:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2018-04-24T16:53:28+03:00</lastmod>
<lastmod>2018-04-25T13:15:38+03:00</lastmod>
<priority>0</priority>
</url>

2
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Tags"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
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2
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Tags"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.40" />
<meta name="generator" content="Hugo 0.40.1" />

2
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@ -26,7 +26,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Tags"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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