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Add notes for 2018-10-13

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Alan Orth 2018-10-13 21:17:20 +03:00
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24
content/posts/2018-10.md
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@ -222,4 +222,28 @@ COPY 10000
- CTA uploaded some infographics that are very tall and their thumbnails disrupt the item lists on the front page and in their communities and collections
- I decided to constrain the max height of these to 200px using CSS ([#392](https://github.com/ilri/DSpace/pull/392))
## 2018-10-13
- Run all system updates on DSpace Test (linode19) and reboot it
- Look through Peter's list of 746 author corrections in OpenRefine
- I first facet by blank, trim whitespace, and then check for weird characters that might be indicative of encoding issues with this GREL:
```
or(
isNotNull(value.match(/.*\uFFFD.*/)),
isNotNull(value.match(/.*\u00A0.*/)),
isNotNull(value.match(/.*\u200A.*/)),
isNotNull(value.match(/.*\u2019.*/)),
isNotNull(value.match(/.*\u00b4.*/))
)
```
- Then I exported and applied them on my local test server:
```
$ ./fix-metadata-values.py -i 2018-10-11-top-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t CORRECT -m 3
```
- I will apply these on CGSpace when I do the other updates tomorrow, as well as double check the high scoring ones to see if they are correct in Sisay's author controlled vocabulary
<!-- vim: set sw=2 ts=2: -->

2
docs/2015-11/index.html
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@ -38,7 +38,7 @@ $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspac
"/>
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docs/2015-12/index.html
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@ -40,7 +40,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
"/>
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docs/2016-01/index.html
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@ -30,7 +30,7 @@ Update GitHub wiki for documentation of maintenance tasks.
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docs/2016-02/index.html
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@ -44,7 +44,7 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
"/>
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docs/2016-03/index.html
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@ -30,7 +30,7 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
"/>
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docs/2016-04/index.html
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@ -34,7 +34,7 @@ Also, I noticed the checker log has some errors we should pay attention to:
"/>
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docs/2016-05/index.html
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@ -38,7 +38,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
"/>
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docs/2016-06/index.html
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@ -36,7 +36,7 @@ Working on second phase of metadata migration, looks like this will work for mov
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docs/2016-07/index.html
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@ -52,7 +52,7 @@ In this case the select query was showing 95 results before the update
"/>
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docs/2016-08/index.html
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@ -46,7 +46,7 @@ $ git rebase -i dspace-5.5
"/>
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docs/2016-09/index.html
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@ -38,7 +38,7 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
"/>
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docs/2016-10/index.html
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@ -46,7 +46,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
"/>
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docs/2016-11/index.html
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@ -30,7 +30,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
"/>
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docs/2016-12/index.html
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@ -54,7 +54,7 @@ Another worrying error from dspace.log is:
"/>
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docs/2017-01/index.html
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@ -30,7 +30,7 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
"/>
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docs/2017-02/index.html
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@ -58,7 +58,7 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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docs/2017-03/index.html
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@ -62,7 +62,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
"/>
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2
docs/2017-04/index.html
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@ -48,7 +48,7 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
"/>
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<meta name="generator" content="Hugo 0.49.2" />

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docs/2017-05/index.html
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@ -14,7 +14,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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docs/2017-06/index.html
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@ -14,7 +14,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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docs/2017-07/index.html
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@ -42,7 +42,7 @@ We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the
"/>
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docs/2017-08/index.html
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@ -62,7 +62,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
"/>
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2
docs/2017-09/index.html
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@ -38,7 +38,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
"/>
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docs/2017-10/index.html
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@ -42,7 +42,7 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
"/>
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docs/2017-11/index.html
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@ -62,7 +62,7 @@ COPY 54701
"/>
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docs/2017-12/index.html
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@ -32,7 +32,7 @@ The list of connections to XMLUI and REST API for today:
"/>
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docs/2018-01/index.html
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@ -170,7 +170,7 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
"/>
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2
docs/2018-02/index.html
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@ -32,7 +32,7 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
"/>
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docs/2018-03/index.html
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@ -26,7 +26,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
"/>
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2
docs/2018-04/index.html
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@ -28,7 +28,7 @@ Catalina logs at least show some memory errors yesterday:
"/>
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2
docs/2018-05/index.html
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@ -40,7 +40,7 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
"/>
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2
docs/2018-06/index.html
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@ -68,7 +68,7 @@ sys 2m7.289s
"/>
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2
docs/2018-07/index.html
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@ -46,7 +46,7 @@ There is insufficient memory for the Java Runtime Environment to continue.
"/>
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2
docs/2018-08/index.html
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@ -54,7 +54,7 @@ I ran all system updates on DSpace Test and rebooted it
"/>
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2
docs/2018-09/index.html
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@ -32,7 +32,7 @@ I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I
"/>
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36
docs/2018-10/index.html
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@ -9,12 +9,12 @@
<meta property="og:description" content="2018-10-01 Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nairobi right now 2018-10-03 I see Moayad was busy collecting item views and downloads from CGSpace yesterday: # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Oct/2018&quot; | awk &#39;{print $1} &#39; | sort | uniq -c | sort -n | tail -n 10 933 40." />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-10/" /><meta property="article:published_time" content="2018-10-01T22:31:54&#43;03:00"/>
<meta property="article:modified_time" content="2018-10-11T11:17:07&#43;03:00"/>
<meta property="article:modified_time" content="2018-10-11T14:25:13&#43;03:00"/>
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2018"/>
<meta name="twitter:description" content="2018-10-01 Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nairobi right now 2018-10-03 I see Moayad was busy collecting item views and downloads from CGSpace yesterday: # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Oct/2018&quot; | awk &#39;{print $1} &#39; | sort | uniq -c | sort -n | tail -n 10 933 40."/>
<meta name="generator" content="Hugo 0.49" />
<meta name="generator" content="Hugo 0.49.2" />
@ -24,9 +24,9 @@
"@type": "BlogPosting",
"headline": "October, 2018",
"url": "https://alanorth.github.io/cgspace-notes/2018-10/",
"wordCount": "1407",
"wordCount": "1519",
"datePublished": "2018-10-01T22:31:54&#43;03:00",
"dateModified": "2018-10-11T11:17:07&#43;03:00",
"dateModified": "2018-10-11T14:25:13&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -344,6 +344,34 @@ COPY 10000
<li>I decided to constrain the max height of these to 200px using CSS (<a href="https://github.com/ilri/DSpace/pull/392">#392</a>)</li>
</ul>
<h2 id="2018-10-13">2018-10-13</h2>
<ul>
<li>Run all system updates on DSpace Test (linode19) and reboot it</li>
<li>Look through Peter&rsquo;s list of 746 author corrections in OpenRefine</li>
<li>I first facet by blank, trim whitespace, and then check for weird characters that might be indicative of encoding issues with this GREL:</li>
</ul>
<pre><code>or(
isNotNull(value.match(/.*\uFFFD.*/)),
isNotNull(value.match(/.*\u00A0.*/)),
isNotNull(value.match(/.*\u200A.*/)),
isNotNull(value.match(/.*\u2019.*/)),
isNotNull(value.match(/.*\u00b4.*/))
)
</code></pre>
<ul>
<li>Then I exported and applied them on my local test server:</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i 2018-10-11-top-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t CORRECT -m 3
</code></pre>
<ul>
<li>I will apply these on CGSpace when I do the other updates tomorrow, as well as double check the high scoring ones to see if they are correct in Sisay&rsquo;s author controlled vocabulary</li>
</ul>
<!-- vim: set sw=2 ts=2: -->

2
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@ -13,7 +13,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

2
docs/categories/index.html
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@ -13,7 +13,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

2
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@ -14,7 +14,7 @@
<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 0.49" />
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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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docs/index.html
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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

2
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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

2
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@ -14,7 +14,7 @@
<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."/>
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@ -14,7 +14,7 @@
<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 0.49" />
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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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@ -14,7 +14,7 @@
<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 0.49" />
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@ -14,7 +14,7 @@
<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."/>
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@ -4,7 +4,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/2018-10/</loc>
<lastmod>2018-10-11T11:17:07+03:00</lastmod>
<lastmod>2018-10-11T14:25:13+03:00</lastmod>
</url>
<url>
@ -189,7 +189,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2018-10-11T11:17:07+03:00</lastmod>
<lastmod>2018-10-11T14:25:13+03:00</lastmod>
<priority>0</priority>
</url>
@ -200,7 +200,7 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/notes/</loc>
<lastmod>2018-10-11T11:17:07+03:00</lastmod>
<lastmod>2018-10-11T14:25:13+03:00</lastmod>
<priority>0</priority>
</url>
@ -212,13 +212,13 @@
<url>
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
<lastmod>2018-10-11T11:17:07+03:00</lastmod>
<lastmod>2018-10-11T14:25:13+03:00</lastmod>
<priority>0</priority>
</url>
<url>
<loc>https://alanorth.github.io/cgspace-notes/tags/</loc>
<lastmod>2018-10-11T11:17:07+03:00</lastmod>
<lastmod>2018-10-11T14:25:13+03:00</lastmod>
<priority>0</priority>
</url>

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@ -14,7 +14,7 @@
<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 0.49" />
<meta name="generator" content="Hugo 0.49.2" />

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