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Add notes for 2021-09-20

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Alan Orth 2021-09-20 17:31:45 +03:00
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35
content/posts/2021-09.md
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@ -176,4 +176,39 @@ $ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 do
$ docker-compose build
```
## 2021-09-20
- I synchronized the production CGSpace PostreSQL, Solr, and Assetstore data with DSpace Test
- Over the weekend a few users reported that they could not log into CGSpace
- I checked LDAP and it seems there is something wrong:
```console
$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "cgspace-ldap-account@cgiarad.org" -W "(sAMAccountName=someaccountnametocheck)"
Enter LDAP Password:
ldap_sasl_bind(SIMPLE): Can't contact LDAP server (-1)
```
- I sent a message to CGNET to ask about the server settings and see if our IP is still whitelisted
- It turns out that CGNET created a new Active Directory server (AZCGNEROOT3.cgiarad.org) and decomissioned the old one last week
- I updated the configuration on CGSpace and confirmed that it is working
- Create another test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:
```console
$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
```
- I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
- According to my notes from [2020-10]({{< relref "2020-10.md" >}}) the account must be in the admin group in order to submit via the REST API
- Run `dspace cleanup -v` process on CGSpace to clean up old bitstreams
- Export lists of authors, donors, and affiliations for Peter Ballantyne to clean up:
```console
localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "dc.contributor.author", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 3 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-09-20-authors.csv WITH CSV HEADER;
COPY 80901
localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.donor", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 248 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-09-20-donors.csv WITH CSV HEADER;
COPY 1274
localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-09-20-affiliations.csv WITH CSV HEADER;
COPY 8091
```
<!-- vim: set sw=2 ts=2: -->

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docs/2020-01/index.html
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@ -30,7 +30,7 @@ I tweeted the CGSpace repository link
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-01/" />
<meta property="article:published_time" content="2020-01-06T10:48:30+02:00" />
<meta property="article:modified_time" content="2020-03-12T12:58:21+02:00" />
<meta property="article:modified_time" content="2021-09-20T15:47:34+03:00" />
@ -68,7 +68,7 @@ I tweeted the CGSpace repository link
"url": "https://alanorth.github.io/cgspace-notes/2020-01/",
"wordCount": "3523",
"datePublished": "2020-01-06T10:48:30+02:00",
"dateModified": "2020-03-12T12:58:21+02:00",
"dateModified": "2021-09-20T15:47:34+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -148,7 +148,7 @@ I tweeted the CGSpace repository link
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>

43
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@ -26,7 +26,7 @@ The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search qu
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-09/" />
<meta property="article:published_time" content="2021-09-01T09:14:07+03:00" />
<meta property="article:modified_time" content="2021-09-17T15:03:28+03:00" />
<meta property="article:modified_time" content="2021-09-19T15:42:23+03:00" />
@ -58,9 +58,9 @@ The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search qu
"@type": "BlogPosting",
"headline": "September, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-09/",
"wordCount": "1221",
"wordCount": "1532",
"datePublished": "2021-09-01T09:14:07+03:00",
"dateModified": "2021-09-17T15:03:28+03:00",
"dateModified": "2021-09-19T15:42:23+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -340,6 +340,43 @@ dspace.log.2021-09-17:15235
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
$ docker-compose build
</code></pre><h2 id="2021-09-20">2021-09-20</h2>
<ul>
<li>I synchronized the production CGSpace PostreSQL, Solr, and Assetstore data with DSpace Test</li>
<li>Over the weekend a few users reported that they could not log into CGSpace
<ul>
<li>I checked LDAP and it seems there is something wrong:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;cgspace-ldap-account@cgiarad.org&quot; -W &quot;(sAMAccountName=someaccountnametocheck)&quot;
Enter LDAP Password:
ldap_sasl_bind(SIMPLE): Can't contact LDAP server (-1)
</code></pre><ul>
<li>I sent a message to CGNET to ask about the server settings and see if our IP is still whitelisted
<ul>
<li>It turns out that CGNET created a new Active Directory server (AZCGNEROOT3.cgiarad.org) and decomissioned the old one last week</li>
<li>I updated the configuration on CGSpace and confirmed that it is working</li>
</ul>
</li>
<li>Create another test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
</code></pre><ul>
<li>I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
<ul>
<li>According to my notes from <a href="/cgspace-notes/2020-10/">2020-10</a> the account must be in the admin group in order to submit via the REST API</li>
</ul>
</li>
<li>Run <code>dspace cleanup -v</code> process on CGSpace to clean up old bitstreams</li>
<li>Export lists of authors, donors, and affiliations for Peter Ballantyne to clean up:</li>
</ul>
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;dc.contributor.author&quot;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 3 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-09-20-authors.csv WITH CSV HEADER;
COPY 80901
localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;cg.contributor.donor&quot;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 248 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-09-20-donors.csv WITH CSV HEADER;
COPY 1274
localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &quot;cg.contributor.affiliation&quot;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-09-20-affiliations.csv WITH CSV HEADER;
COPY 8091
</code></pre><!-- raw HTML omitted -->

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@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

2
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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -439,7 +439,7 @@ COPY 20994
&lt;li&gt;Last week Altmetric responded about the &lt;a href=&#34;https://hdl.handle.net/10568/97087&#34;&gt;item&lt;/a&gt; that had a lower score than than its DOI
&lt;ul&gt;
&lt;li&gt;The score is now linked to the DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://handle.hdl.net/10568/91278&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has now also linked to the score for its DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://hdl.handle.net/10568/91278&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has now also linked to the score for its DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://hdl.handle.net/10568/81236&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has also been fixed&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;

2
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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

4
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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />
@ -154,7 +154,7 @@
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>

2
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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -439,7 +439,7 @@ COPY 20994
&lt;li&gt;Last week Altmetric responded about the &lt;a href=&#34;https://hdl.handle.net/10568/97087&#34;&gt;item&lt;/a&gt; that had a lower score than than its DOI
&lt;ul&gt;
&lt;li&gt;The score is now linked to the DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://handle.hdl.net/10568/91278&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has now also linked to the score for its DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://hdl.handle.net/10568/91278&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has now also linked to the score for its DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://hdl.handle.net/10568/81236&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has also been fixed&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />
@ -169,7 +169,7 @@
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -439,7 +439,7 @@ COPY 20994
&lt;li&gt;Last week Altmetric responded about the &lt;a href=&#34;https://hdl.handle.net/10568/97087&#34;&gt;item&lt;/a&gt; that had a lower score than than its DOI
&lt;ul&gt;
&lt;li&gt;The score is now linked to the DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://handle.hdl.net/10568/91278&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has now also linked to the score for its DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://hdl.handle.net/10568/91278&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has now also linked to the score for its DOI&lt;/li&gt;
&lt;li&gt;Another &lt;a href=&#34;https://hdl.handle.net/10568/81236&#34;&gt;item&lt;/a&gt; that had the same problem in 2019 has also been fixed&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />
@ -169,7 +169,7 @@
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>

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@ -10,7 +10,7 @@
<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="2021-09-17T15:03:28+03:00" />
<meta property="og:updated_time" content="2021-09-20T15:47:34+03:00" />

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