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106
content/posts/2022-11.md
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@ -247,4 +247,110 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
- I did some more work on my `post-ciat-pdfs.py` script and tested uploading the items to my local DSpace and DSpace Test
- Then I ran the script on CGSpace, uploading ~1,500 PDFs to to existing items
## 2022-11-25
- Tony Murray, who is working on IFPRI's CGSpace integration, emailed me to ask some questions about the REST API
- Oh no, I realized there is a logic issue with the PDFbox cropbox code I added a few weeks ago:
```console
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace filter-media -p "ImageMagick PDF Thumbnail" -v -f -i 10568/77010
The following MediaFilters are enabled:
Full Filter Name: org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter
org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter
Loading @mire database changes for module MQM
Changes have been processed
IM Thumbnail tropentag2016_marshall.pdf is replacable.
File: tropentag2016_marshall.pdf.jpg
ERROR filtering, skipping bitstream:
Item Handle: 10568/77010
Bundle Name: ORIGINAL
File Size: 1486580
Checksum: 1ad66d918a56a5e84667386e1a32e352 (MD5)
Asset Store: 0
java.lang.IndexOutOfBoundsException: 1-based index out of bounds: 2
java.lang.IndexOutOfBoundsException: 1-based index out of bounds: 2
at org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:325)
at org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:248)
at org.apache.pdfbox.pdmodel.PDDocument.getPage(PDDocument.java:1543)
at org.dspace.app.mediafilter.ImageMagickThumbnailFilter.getImageFile(ImageMagickThumbnailFilter.java:167)
at org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.getDestinationStream(ImageMagickPdfThumbnailFilter.java:27)
at com.atmire.dspace.app.mediafilter.AtmireMediaFilter.processBitstream(AtmireMediaFilter.java:103)
at com.atmire.dspace.app.mediafilter.AtmireMediaFilterServiceImpl.filterBitstream(AtmireMediaFilterServiceImpl.java:61)
at org.dspace.app.mediafilter.MediaFilterServiceImpl.filterItem(MediaFilterServiceImpl.java:181)
at org.dspace.app.mediafilter.MediaFilterServiceImpl.applyFiltersItem(MediaFilterServiceImpl.java:159)
at org.dspace.app.mediafilter.MediaFilterCLITool.main(MediaFilterCLITool.java:232)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
```
- Salem gave me a list of CGSpace collections that have double spaces in the names
- Normally this would only be a minor annoyance, but he discovered that the REST API seems to trim the spaces, which causes an issue when trying to reference them!
- He sent me a list of about ten collection UUIDs so I fixed them
- I found a bunch of LIVES presentations on CGSpace that have presentations on SlideShare with incorrect licenses... I updated about fifty of them
## 2022-11-26
- Sync DSpace Test with CGSpace
- I increased the session timeout in Tomcat from thirty minutes to sixty, as requested by Maria a few weeks ago
- See: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/-/issues/44
- I re-built DSpace on CGSpace, ran all updates, and rebooted the machine
- Then after coming back up the handle server won't start
- The `handle-server.log` file shows:
```console
Shutting down...
"2022/11/26 02:12:17 CET" 25 Rotating log files
Error: null
(see the error log for details.)
```
- In the `error.log` file I see:
```console
"2022/11/26 02:12:18 CET" 25 Started new run.
java.lang.UnsupportedOperationException
at java.lang.Runtime.runFinalizersOnExit(Runtime.java:287)
at java.lang.System.runFinalizersOnExit(System.java:1059)
at net.handle.server.Main.initialize(Main.java:124)
at net.handle.server.Main.main(Main.java:75)
Shutting down...
```
- Ah, it seems to be due to an [issue in OpenJDK 1.8.0_352](https://groups.google.com/g/dspace-tech/c/PqjfA5mqG4w/m/FhxI5oXhFwAJ?pli=1)
- I see the server upgraded to the new JDK version on 2022-11-10:
```console
Upgrade: openjdk-8-jdk-headless:amd64 (8u342-b07-0ubuntu1~20.04, 8u352-ga-1~20.04), openjdk-8-jre-headless:amd64 (8u342-b07-0ubuntu1~20.04, 8u352-ga-1~20.04)
End-Date: 2022-11-10 04:10:45
```
- As highlighted in the dspace-tech mailing list thread above, [this OpenJDK release deprecated `Runtime.runFinalizersOnExit`](https://mail.openjdk.org/pipermail/jdk8u-dev/2022-October/015706.html):
```console
- JDK-8287132: Retire Runtime.runFinalizersOnExit so that it always throws UOE
```
- I downloaded the previous versions of the packages from Launchpad:
```console
# wget https://launchpad.net/~openjdk-security/+archive/ubuntu/ppa/+build/24195357/+files/openjdk-8-jdk-headless_8u342-b07-0ubuntu1~20.04_amd64.deb
# wget https://launchpad.net/~openjdk-security/+archive/ubuntu/ppa/+build/24195357/+files/openjdk-8-jre-headless_8u342-b07-0ubuntu1~20.04_amd64.deb
# dpkg -i openjdk-8-j*8u342-b07*.deb
```
- Then the handle-server process starts up fine, so I held these OpenJDK versions for now:
```console
# apt-mark hold openjdk-8-jdk-headless:amd64 apt-mark hold openjdk-8-jre-headless:amd64
openjdk-8-jdk-headless set on hold.
openjdk-8-jre-headless set on hold.
```
- Start a harvest on AReS
<!-- vim: set sw=2 ts=2: -->

107
docs/2022-11/index.html
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@ -24,7 +24,7 @@ I reverted the Cocoon autosave change because it was more of a nuissance that Pe
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-11/" />
<meta property="article:published_time" content="2022-11-01T09:11:36+03:00" />
<meta property="article:modified_time" content="2022-11-23T17:10:47+03:00" />
<meta property="article:modified_time" content="2022-11-24T17:41:34+03:00" />
@ -54,9 +54,9 @@ I reverted the Cocoon autosave change because it was more of a nuissance that Pe
"@type": "BlogPosting",
"headline": "November, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-11/",
"wordCount": "1785",
"wordCount": "2221",
"datePublished": "2022-11-01T09:11:36+03:00",
"dateModified": "2022-11-23T17:10:47+03:00",
"dateModified": "2022-11-24T17:41:34+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -425,6 +425,107 @@ I reverted the Cocoon autosave change because it was more of a nuissance that Pe
</ul>
</li>
</ul>
<h2 id="2022-11-25">2022-11-25</h2>
<ul>
<li>Tony Murray, who is working on IFPRI&rsquo;s CGSpace integration, emailed me to ask some questions about the REST API</li>
<li>Oh no, I realized there is a logic issue with the PDFbox cropbox code I added a few weeks ago:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</span> -v -f -i 10568/77010
</span></span><span style="display:flex;"><span>The following MediaFilters are enabled:
</span></span><span style="display:flex;"><span>Full Filter Name: org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter
</span></span><span style="display:flex;"><span>org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter
</span></span><span style="display:flex;"><span>Loading @mire database changes for module MQM
</span></span><span style="display:flex;"><span>Changes have been processed
</span></span><span style="display:flex;"><span>IM Thumbnail tropentag2016_marshall.pdf is replacable.
</span></span><span style="display:flex;"><span>File: tropentag2016_marshall.pdf.jpg
</span></span><span style="display:flex;"><span>ERROR filtering, skipping bitstream:
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span> Item Handle: 10568/77010
</span></span><span style="display:flex;"><span> Bundle Name: ORIGINAL
</span></span><span style="display:flex;"><span> File Size: 1486580
</span></span><span style="display:flex;"><span> Checksum: 1ad66d918a56a5e84667386e1a32e352 (MD5)
</span></span><span style="display:flex;"><span> Asset Store: 0
</span></span><span style="display:flex;"><span>java.lang.IndexOutOfBoundsException: 1-based index out of bounds: 2
</span></span><span style="display:flex;"><span>java.lang.IndexOutOfBoundsException: 1-based index out of bounds: 2
</span></span><span style="display:flex;"><span> at org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:325)
</span></span><span style="display:flex;"><span> at org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:248)
</span></span><span style="display:flex;"><span> at org.apache.pdfbox.pdmodel.PDDocument.getPage(PDDocument.java:1543)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.ImageMagickThumbnailFilter.getImageFile(ImageMagickThumbnailFilter.java:167)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.getDestinationStream(ImageMagickPdfThumbnailFilter.java:27)
</span></span><span style="display:flex;"><span> at com.atmire.dspace.app.mediafilter.AtmireMediaFilter.processBitstream(AtmireMediaFilter.java:103)
</span></span><span style="display:flex;"><span> at com.atmire.dspace.app.mediafilter.AtmireMediaFilterServiceImpl.filterBitstream(AtmireMediaFilterServiceImpl.java:61)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.MediaFilterServiceImpl.filterItem(MediaFilterServiceImpl.java:181)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.MediaFilterServiceImpl.applyFiltersItem(MediaFilterServiceImpl.java:159)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.MediaFilterCLITool.main(MediaFilterCLITool.java:232)
</span></span><span style="display:flex;"><span> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
</span></span><span style="display:flex;"><span> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
</span></span><span style="display:flex;"><span> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
</span></span><span style="display:flex;"><span> at java.lang.reflect.Method.invoke(Method.java:498)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</span></span></code></pre></div><ul>
<li>Salem gave me a list of CGSpace collections that have double spaces in the names
<ul>
<li>Normally this would only be a minor annoyance, but he discovered that the REST API seems to trim the spaces, which causes an issue when trying to reference them!</li>
<li>He sent me a list of about ten collection UUIDs so I fixed them</li>
</ul>
</li>
<li>I found a bunch of LIVES presentations on CGSpace that have presentations on SlideShare with incorrect licenses&hellip; I updated about fifty of them</li>
</ul>
<h2 id="2022-11-26">2022-11-26</h2>
<ul>
<li>Sync DSpace Test with CGSpace</li>
<li>I increased the session timeout in Tomcat from thirty minutes to sixty, as requested by Maria a few weeks ago
<ul>
<li>See: <a href="https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/-/issues/44">https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/-/issues/44</a></li>
</ul>
</li>
<li>I re-built DSpace on CGSpace, ran all updates, and rebooted the machine
<ul>
<li>Then after coming back up the handle server won&rsquo;t start</li>
<li>The <code>handle-server.log</code> file shows:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>Shutting down...
</span></span><span style="display:flex;"><span>&#34;2022/11/26 02:12:17 CET&#34; 25 Rotating log files
</span></span><span style="display:flex;"><span>Error: null
</span></span><span style="display:flex;"><span> (see the error log for details.)
</span></span></code></pre></div><ul>
<li>In the <code>error.log</code> file I see:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>&#34;2022/11/26 02:12:18 CET&#34; 25 Started new run.
</span></span><span style="display:flex;"><span>java.lang.UnsupportedOperationException
</span></span><span style="display:flex;"><span> at java.lang.Runtime.runFinalizersOnExit(Runtime.java:287)
</span></span><span style="display:flex;"><span> at java.lang.System.runFinalizersOnExit(System.java:1059)
</span></span><span style="display:flex;"><span> at net.handle.server.Main.initialize(Main.java:124)
</span></span><span style="display:flex;"><span> at net.handle.server.Main.main(Main.java:75)
</span></span><span style="display:flex;"><span>Shutting down...
</span></span></code></pre></div><ul>
<li>Ah, it seems to be due to an <a href="https://groups.google.com/g/dspace-tech/c/PqjfA5mqG4w/m/FhxI5oXhFwAJ?pli=1">issue in OpenJDK 1.8.0_352</a></li>
<li>I see the server upgraded to the new JDK version on 2022-11-10:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>Upgrade: openjdk-8-jdk-headless:amd64 (8u342-b07-0ubuntu1~20.04, 8u352-ga-1~20.04), openjdk-8-jre-headless:amd64 (8u342-b07-0ubuntu1~20.04, 8u352-ga-1~20.04)
</span></span><span style="display:flex;"><span>End-Date: 2022-11-10 04:10:45
</span></span></code></pre></div><ul>
<li>As highlighted in the dspace-tech mailing list thread above, <a href="https://mail.openjdk.org/pipermail/jdk8u-dev/2022-October/015706.html">this OpenJDK release deprecated <code>Runtime.runFinalizersOnExit</code></a>:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span> - JDK-8287132: Retire Runtime.runFinalizersOnExit so that it always throws UOE
</span></span></code></pre></div><ul>
<li>I downloaded the previous versions of the packages from Launchpad:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># wget https://launchpad.net/~openjdk-security/+archive/ubuntu/ppa/+build/24195357/+files/openjdk-8-jdk-headless_8u342-b07-0ubuntu1~20.04_amd64.deb
</span></span><span style="display:flex;"><span># wget https://launchpad.net/~openjdk-security/+archive/ubuntu/ppa/+build/24195357/+files/openjdk-8-jre-headless_8u342-b07-0ubuntu1~20.04_amd64.deb
</span></span><span style="display:flex;"><span># dpkg -i openjdk-8-j*8u342-b07*.deb
</span></span></code></pre></div><ul>
<li>Then the handle-server process starts up fine, so I held these OpenJDK versions for now:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># apt-mark hold openjdk-8-jdk-headless:amd64 apt-mark hold openjdk-8-jre-headless:amd64
</span></span><span style="display:flex;"><span>openjdk-8-jdk-headless set on hold.
</span></span><span style="display:flex;"><span>openjdk-8-jre-headless set on hold.
</span></span></code></pre></div><ul>
<li>Start a harvest on AReS</li>
</ul>
<!-- 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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+03:00" />

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<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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+03:00" />

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<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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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="2022-11-23T17:10:47+03:00" />
<meta property="og:updated_time" content="2022-11-24T17:41:34+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" />
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