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<meta property="og:description" content="2023-09-02
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Export CGSpace to check for missing Initiative collection mappings
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Start a harvest on AReS
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<meta name="twitter:description" content="2023-09-02
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Export CGSpace to check for missing Initiative collection mappings
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Start a harvest on AReS
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<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/2023-09/">September, 2023</a></h2>
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<time datetime="2023-09-02T17:29:36+03:00">Sat Sep 02, 2023</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2023-09-02">2023-09-02</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative collection mappings</li>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2023-09-03">2023-09-03</h2>
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<ul>
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<li>I figured out how to use Altmetric and Dimensions badges in the DSpace Angular frontend
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<ul>
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<li>It still feels hacky, but using <a href="https://stackoverflow.com/questions/41936631/how-to-trigger-the-function-after-dom-markup-is-loaded-in-angular-style-applicat">AfterViewInit</a>, and importing the Altmetric <code>embed.js</code> in the component works</li>
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<li>The style on mobile also needs work…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-09-06">2023-09-06</h2>
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<ul>
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<li>Discussion with Marie about finalizing the output types list on GitHub
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<ul>
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<li>I did some review and cleanup in preparation for publishing the new list</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-09-07">2023-09-07</h2>
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<ul>
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<li>Export CGSpace to start doing a review of the metadata</li>
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<li>First I will start by extracting all items with DOIs, along with some fields I can compare against Crossref:</li>
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</ul>
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<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>$ csvgrep -c <span style="color:#e6db74">'cg.identifier.doi[en_US]'</span> -r <span style="color:#e6db74">'doi.org'</span> ~/Downloads/2023-09-07-cgspace.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c 'id,dc.title[en_US],dcterms.issued[en_US],dcterms.available[en_US],cg.issn[en_US],cg.isbn[en_US],cg.volume[en_US],cg.issue[en_US],cg.number[en_US],dcterms.extent[en_US],cg.identifier.doi[en_US],cg.reviewStatus[en_US],cg.isijournal[en_US],dcterms.license[en_US],dcterms.accessRights[en_US],dcterms.type[en_US],dc.identifier.uri[en_US]' \
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</span></span><span style="display:flex;"><span> > /tmp/2023-09-07-cgspace-dois.csv
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</span></span><span style="display:flex;"><span>$ csvgrep -c <span style="color:#e6db74">'cg.identifier.doi[en_US]'</span> -r <span style="color:#e6db74">'doi.org'</span> ~/Downloads/2023-09-07-cgspace.csv | csvcut -c <span style="color:#e6db74">'cg.identifier.doi[en_US]'</span> | sed 1d > /tmp/2023-09-07-cgspace-dois.txt
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</span></span></code></pre></div><ul>
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<li>Then I resolved the DOIs from Crossref:</li>
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</ul>
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<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>$ ./ilri/crossref_doi_lookup.py -i /tmp/2023-09-07-cgspace-dois.txt -o /tmp/2023-09-07-cgspace-dois-results.csv -e a.orth@cgiar.org
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</span></span></code></pre></div><ul>
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<li>A user emailed to ask about uploading a 180MB PDF to CGSpace
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<ul>
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<li>I used GhostScript to try reducing it using the <code>screen</code>, <code>ebook</code> and <code>prepress</code> presets:</li>
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</ul>
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</li>
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</ul>
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<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>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>primer-screen.pdf Primer<span style="color:#ae81ff">\ \(</span>digital<span style="color:#ae81ff">\)</span>_Climate-<span style="color:#ae81ff">\ </span>smart<span style="color:#ae81ff">\ </span>and<span style="color:#ae81ff">\ </span>regenerative<span style="color:#ae81ff">\ </span>agriculture<span style="color:#ae81ff">\ </span>in<span style="color:#ae81ff">\ </span>climate<span style="color:#ae81ff">\ </span>change<span style="color:#ae81ff">\ </span>adaptation.pdf
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</span></span><span style="display:flex;"><span>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/ebook -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>primer-ebook.pdf Primer<span style="color:#ae81ff">\ \(</span>digital<span style="color:#ae81ff">\)</span>_Climate-<span style="color:#ae81ff">\ </span>smart<span style="color:#ae81ff">\ </span>and<span style="color:#ae81ff">\ </span>regenerative<span style="color:#ae81ff">\ </span>agriculture<span style="color:#ae81ff">\ </span>in<span style="color:#ae81ff">\ </span>climate<span style="color:#ae81ff">\ </span>change<span style="color:#ae81ff">\ </span>adaptation.pdf
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</span></span><span style="display:flex;"><span>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/prepress -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>primer-prepress.pdf Primer<span style="color:#ae81ff">\ \(</span>digital<span style="color:#ae81ff">\)</span>_Climate-<span style="color:#ae81ff">\ </span>smart<span style="color:#ae81ff">\ </span>and<span style="color:#ae81ff">\ </span>regenerative<span style="color:#ae81ff">\ </span>agriculture<span style="color:#ae81ff">\ </span>in<span style="color:#ae81ff">\ </span>climate<span style="color:#ae81ff">\ </span>change<span style="color:#ae81ff">\ </span>adaptation.pdf
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</span></span></code></pre></div><ul>
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<li>The <code>prepress</code> one is 300DPI and looks visually identical to the original, so I proposed that we use that one</li>
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</ul>
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<h2 id="2023-09-08">2023-09-08</h2>
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<ul>
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<li>I did a review of the metadata for our items with DOIs, comparing with data from Crossref
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<ul>
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<li>I spot checked a handful of issue / online dates and licenses, and saw that Crossref’s dates are always more accurate than ours when they differ</li>
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<li>I also filled in some missing volumes, issues, ISSNs, and extents</li>
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<li>This results in 14,000 changes to existing items, which will take several days to import unfortunately</li>
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<li>After eight hours the first file is only about 2/3 finished… sigh</li>
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</ul>
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</li>
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<li>Meet with Peter to discuss changes to the DSpace 7 test
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<ul>
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<li>Minor updates to submission forms and some new ideas for the home page and item page</li>
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</ul>
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</li>
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<li>I figured out how to use a themed home page component and add a cards UI to our CGSpace theme</li>
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</ul>
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<h2 id="2023-09-09">2023-09-09</h2>
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<ul>
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<li>I can’t believe that almost 18 hours later the first CSV import with 5,000 changes is not done…</li>
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<li>Run all system updates on CGSpace and reboot it, as it had been two months since the last time</li>
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</ul>
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<h2 id="2023-09-10">2023-09-10</h2>
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<ul>
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<li>Minor work on the DSpace 7 home page</li>
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</ul>
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<h2 id="2023-09-11">2023-09-11</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative collection mappings</li>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2023-09-12">2023-09-12</h2>
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<ul>
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<li>Minor work on DSpace 7 home page</li>
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<li>Minor work on CG Core types
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<ul>
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<li>I published a new HTML version of the updated IPtypes and archived the current version as v2.0.0 so we can still reference it</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-09-13">2023-09-13</h2>
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<ul>
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<li>Stefano reminded me about the updated OAI MODS mappings on CGSpace so I re-applied them on DSpace Test and updated the OAI index so he could confirm
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<ul>
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<li>Now I’m ready to put it on CGSpace if he confirms</li>
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</ul>
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</li>
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<li>I created a basic theme for CIP on DSpace 7
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<ul>
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<li>While doing that I noticed that a bunch of CIP bitstreams didn’t have the latest 500px thumbnails so I re-ran filter-media on a handful of their collections</li>
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</ul>
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</li>
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<li>I had two occurrences of an OOM kill of the Tomcat 9 java process on DSpace 7 test tonight
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<ul>
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<li>Once while doing a Discovery index, the other while doing filter media</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-09-15">2023-09-15</h2>
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<ul>
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<li>Discuss issues with the Altmetric API with the Altmetric support team
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<ul>
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<li>Apparently we can use a different API, the <a href="https://www.altmetric.com/explorer/documentation/api">Explorer API</a>, since we already have access to the Explorer dashboard</li>
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</ul>
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</li>
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<li>I reduced the Solr heap size on DSpace 7 from 3GB to 2GB
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<ul>
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<li>Apparentlty I already did this from 4GB to 3GB a few months ago</li>
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<li>The Solr admin interface was showing Solr taking ~1GB of RAM so I think this should be safe</li>
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</ul>
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</li>
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<li>Mark on DSpace Slack said he uses PM2’s <code>--max-memory-restart</code> so the processes restart when they hit the limit
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<ul>
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<li>Also, he said he had to reduce <code>cache:serverSide:botCache:max</code> from 1000 to 500 to cache less SSR pages in memory</li>
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</ul>
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</li>
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<li>I decided to try deploying DSpace 7 Test on a Hetzner server with 64GB RAM, 6 CPUs, and 2x512GB NVMe SSD</li>
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</ul>
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<h2 id="2023-09-16">2023-09-16</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative collection mappings</li>
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<li>Start a harvest on AReS</li>
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<li>Configure the privacy policy page on DSpace 7 using a themed component with the text from our DSpace 6 site</li>
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</ul>
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2023-09/">September, 2023</a></li>
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<li><a href="/cgspace-notes/2023-08/">August, 2023</a></li>
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<li><a href="/cgspace-notes/2023-07/">July, 2023</a></li>
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<li><a href="/cgspace-notes/2023-06/">June, 2023</a></li>
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<li><a href="/cgspace-notes/2023-05/">May, 2023</a></li>
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<h4>Links</h4>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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