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<meta property="og:description" content="2023-04-02
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Run all system updates on CGSpace and reboot it
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I exported CGSpace to CSV to check for any missing Initiative collection mappings
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I also did a check for missing country/region mappings with csv-metadata-quality
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Start a harvest on AReS
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<meta name="twitter:title" content="April, 2023"/>
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<meta name="twitter:description" content="2023-04-02
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Run all system updates on CGSpace and reboot it
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I exported CGSpace to CSV to check for any missing Initiative collection mappings
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I also did a check for missing country/region mappings with csv-metadata-quality
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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/2023-04/">April, 2023</a></h2>
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<time datetime="2023-04-02T08:19:36+03:00">Sun Apr 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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<h2 id="2023-04-02">2023-04-02</h2>
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<ul>
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<li>Run all system updates on CGSpace and reboot it</li>
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<li>I exported CGSpace to CSV to check for any missing Initiative collection mappings
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<ul>
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<li>I also did a check for missing country/region mappings with csv-metadata-quality</li>
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</ul>
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</li>
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<li>Start a harvest on AReS</li>
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</ul>
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<ul>
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<li>I’m starting to get annoyed at my shell script for doing ImageMagick tests and looking to re-write it in something object oriented like Python
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<ul>
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<li>There doesn’t seem to be an official ImageMagick Python binding on pypi.org, perhaps I can use <a href="https://docs.wand-py.org">Wand</a>?</li>
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</ul>
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</li>
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<li>Testing Wand in Python:</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">from</span> wand.image <span style="color:#f92672">import</span> Image
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">with</span> Image(filename<span style="color:#f92672">=</span><span style="color:#e6db74">'data/10568-103447.pdf[0]'</span>, resolution<span style="color:#f92672">=</span><span style="color:#ae81ff">144</span>) <span style="color:#66d9ef">as</span> first_page:
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</span></span><span style="display:flex;"><span> print(first_page<span style="color:#f92672">.</span>height)
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</span></span></code></pre></div><ul>
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<li>I spent more time re-working my thumbnail scripts to compare the resized images and other minor changes
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<ul>
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<li>I am realizing that doing the thumbnails directly from the source improves the ssimulacra2 score by 1-3% points compared to DSpace’s method of creating a lossy supersample followed by a lossy resized thumbnail</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-04-03">2023-04-03</h2>
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<ul>
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<li>The harvest on AReS that I started yesterday never finished, and actually seems to have died…
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<ul>
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<li>Also, Fabio and Patrizio from Alliance emailed me to ask if there is something wrong with the REST API because they are having problems</li>
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<li>I stopped the harvest and started the plugins to get the remaining items via the sitemap…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-04-04">2023-04-04</h2>
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<ul>
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<li>Presentation about CGSpace metadata, controlled vocabularies, and curation to Pooja’s communications and development team at UNEP
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<ul>
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<li>I uploaded the presentation to CGSpace here: <a href="https://hdl.handle.net/10568/129896">https://hdl.handle.net/10568/129896</a></li>
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</ul>
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</li>
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<li>Someone from the system organization contacted me to ask how to download a few thousand PDFs from a spreadsheet with DOIs and Handles</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>$ csvcut -c Handle ~/Downloads/2023-04-04-Donald.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | sed \
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</span></span><span style="display:flex;"><span> -e 1d \
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</span></span><span style="display:flex;"><span> -e 's_https://hdl.handle.net/__' \
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</span></span><span style="display:flex;"><span> -e 's_https://cgspace.cgiar.org/handle/__' \
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</span></span><span style="display:flex;"><span> -e 's_http://hdl.handle.net/__' \
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</span></span><span style="display:flex;"><span> | sort -u > /tmp/handles.txt
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</span></span></code></pre></div><ul>
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<li>Then I used the <code>get_dspace_pdfs.py</code> script to download them</li>
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</ul>
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<h2 id="2023-04-05">2023-04-05</h2>
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<ul>
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<li>After some cleanup on Donald’s DOIs I started the <code>get_scihub_pdfs.py</code> script</li>
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</ul>
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<h2 id="2023-04-06">2023-04-06</h2>
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<ul>
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<li>I did some more work to cleanup and streamline my next generation of DSpace thumbnail testing scripts
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<ul>
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<li>I think I found a bug in ImageMagick 7.1.1.5 where CMYK to sRGB conversion fails if we use image operations like <code>-density</code> or <code>-define</code> before reading the input file</li>
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<li>I started <a href="https://github.com/ImageMagick/ImageMagick/discussions/6234">a discussion on the ImageMagick GitHub</a> to ask</li>
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</ul>
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</li>
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<li>Yesterday I started downloading the rest of the PDFs from Donald, those that had DOIs
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<ul>
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<li>As a measure of caution, I extracted the list of DOIs and used my <code>crossref_doi_lookup.py</code> script to get their licenses from Crossref:</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>$ ./ilri/crossref_doi_lookup.py -e xxxx@i.org -i /tmp/dois.txt -o /tmp/donald-crossref-dois.csv -d
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</span></span></code></pre></div><ul>
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<li>Then I did some CSV manipulation to extract the DOIs that were Creative Commons licensed, excluding any that were “No Derivatives”, and re-formatting the DOIs:</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>$ csvcut -c doi,license /tmp/donald-crossref-dois.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvgrep -c license -m 'creativecommons' \
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</span></span><span style="display:flex;"><span> | csvgrep -c license -i -r 'by-(nd|nc-nd)' \
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</span></span><span style="display:flex;"><span> | sed -e 's_^10_https://doi.org/10_' \
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</span></span><span style="display:flex;"><span> -e 's/\(am\|tdm\|unspecified\|vor\): //' \
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</span></span><span style="display:flex;"><span> | tee /tmp/donald-open-dois.csv \
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</span></span><span style="display:flex;"><span> | wc -l
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</span></span><span style="display:flex;"><span>4268
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</span></span></code></pre></div><ul>
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<li>From those I filtered for the DOIs for which I had downloaded PDFs, in the <code>filename</code> column of the Sci-Hub script and copied them to a separate directory:</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>$ <span style="color:#66d9ef">for</span> file in <span style="color:#66d9ef">$(</span>csvjoin -c doi /tmp/donald-doi-pdfs.csv /tmp/donald-open-dois.csv | csvgrep -c filename -i -r <span style="color:#e6db74">'^$'</span> | csvcut -c filename | sed 1d<span style="color:#66d9ef">)</span>; <span style="color:#66d9ef">do</span> cp --reflink<span style="color:#f92672">=</span>always <span style="color:#e6db74">"</span>$file<span style="color:#e6db74">"</span> <span style="color:#e6db74">"creative-commons-licensed/</span>$file<span style="color:#e6db74">"</span>; <span style="color:#66d9ef">done</span>
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</span></span></code></pre></div><ul>
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<li>I used BTRFS copy-on-write via reflinks to make sure I didn’t duplicate the files :-D</li>
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<li>I ran out of time and had to stop the process around 3,127 PDFs
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<ul>
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<li>I zipped them up and sent them to the others, along with a CSV of the DOIs, PDF filenames, and licenses</li>
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</ul>
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</li>
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</ul>
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<section class="sidebar-module">
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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/2023-04/">April, 2023</a></li>
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<li><a href="/cgspace-notes/2023-03/">March, 2023</a></li>
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<li><a href="/cgspace-notes/2023-02/">February, 2023</a></li>
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<li><a href="/cgspace-notes/2023-01/">January, 2023</a></li>
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<li><a href="/cgspace-notes/2022-12/">December, 2022</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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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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