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<meta property="og:title" content="November, 2022" />
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<meta property="og:description" content="2022-11-01
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Last night I re-synced DSpace 7 Test from CGSpace
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I also updated all my local 7_x-dev branches on the latest upstreams
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I spent some time updating the authorizations in Alliance collections
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I want to make sure they use groups instead of individuals where possible!
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I reverted the Cocoon autosave change because it was more of a nuissance that Peter can’t upload CSVs from the web interface and is a very low severity security issue
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<meta name="twitter:title" content="November, 2022"/>
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<meta name="twitter:description" content="2022-11-01
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Last night I re-synced DSpace 7 Test from CGSpace
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I also updated all my local 7_x-dev branches on the latest upstreams
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I spent some time updating the authorizations in Alliance collections
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I want to make sure they use groups instead of individuals where possible!
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I reverted the Cocoon autosave change because it was more of a nuissance that Peter can’t upload CSVs from the web interface and is a very low severity security issue
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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/2022-11/">November, 2022</a></h2>
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<time datetime="2022-11-01T09:11:36+03:00">Tue Nov 01, 2022</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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</header>
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<h2 id="2022-11-01">2022-11-01</h2>
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<ul>
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<li>Last night I re-synced DSpace 7 Test from CGSpace
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<ul>
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<li>I also updated all my local <code>7_x-dev</code> branches on the latest upstreams</li>
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</ul>
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</li>
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<li>I spent some time updating the authorizations in Alliance collections
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<ul>
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<li>I want to make sure they use groups instead of individuals where possible!</li>
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</ul>
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</li>
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<li>I reverted the Cocoon autosave change because it was more of a nuissance that Peter can’t upload CSVs from the web interface and is a very low severity security issue</li>
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</ul>
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<ul>
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<li>I ran FixLowQualityThumbnails from cgspace-java-helpers on some large collections on CGSpace and ended up fixing 194 items!</li>
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<li>I did some minor checking and uploaded twenty-four IFPRI outputs for the Initiatives to DSpace Test</li>
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<li>Tim merged my <a href="https://github.com/DSpace/DSpace/pull/8553">pull request to override the ImageMagick PDF density in DSpace 7</a>
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<ul>
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<li>I ported it to DSpace 6.x and submitted a pull request: <a href="https://github.com/DSpace/DSpace/pull/8560">https://github.com/DSpace/DSpace/pull/8560</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-11-02">2022-11-02</h2>
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<ul>
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<li>I joined the FAO–CGIAR AGROVOC results sharing meeting
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<ul>
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<li>From June to October, 2022 we suggested 39 new keywords, added 27 to AGROVOC, 4 rejected, and 9 still under discussion</li>
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</ul>
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</li>
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<li>Doing duplicate check on IFPRI’s batch upload and I found one duplicate uploaded by IWMI earlier this year
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<ul>
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<li>I will update the metadata of that item and map it to the correct Initiative collection</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-11-03">2022-11-03</h2>
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<ul>
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<li>I added countries to the twenty-three IFPRI items in OpenRefine based on their titles and abstracts (using the Jython trick I learned a few months ago), then added regions using csv-metadata-quality, and uploaded them to CGSpace</li>
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<li>I exported a list of collections from CGSpace so I can run the thumbnail fixes on each, as we seem to have issues when doing it on (some) large communities like the CRP community:</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>localhost/dspace= ☘ \COPY (SELECT ds6_collection2collectionhandle(uuid) AS collection FROM collection) to /tmp/collections.txt
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</span></span><span style="display:flex;"><span>COPY 1268
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</span></span></code></pre></div><ul>
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<li>Then I started a test run on DSpace Test:</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">while</span> read -r collection; <span style="color:#66d9ef">do</span> chrt -b <span style="color:#ae81ff">0</span> dspace dsrun io.github.ilri.cgspace.scripts.FixLowQualityThumbnails $collection | tee -a /tmp/FixLowQualityThumbnails.log; <span style="color:#66d9ef">done</span> < /tmp/collections.txt
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</span></span></code></pre></div><ul>
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<li>I’ll be curious to check the log after it’s all done.
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<ul>
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<li>After a few hours I see:</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ grep -c <span style="color:#e6db74">'Action: remove'</span> /tmp/FixLowQualityThumbnails.log
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</span></span><span style="display:flex;"><span>626
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</span></span></code></pre></div><ul>
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<li>Not bad, because last week I did a more manual selection of collections and deleted ~200
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<ul>
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<li>I will replicate this on CGSpace soon, and also try the FixJpgJpgThumbnails tool</li>
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</ul>
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</li>
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<li>I see that the CIAT Library is still up, so I should really grab all the PDFs before they shut that old server down
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<ul>
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<li>Export a list of items with PDFs linked there:</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>localhost/dspacetest= ☘ \COPY (SELECT dspace_object_id,text_value FROM metadatavalue WHERE metadata_field_id=219 AND text_value LIKE '%ciat-library%') to /tmp/ciat-library-items.csv;
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</span></span><span style="display:flex;"><span>COPY 4621
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</span></span></code></pre></div><ul>
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<li>After stripping the page numbers off I see there are only about 2,700 unique files, and we have to filter the dead JSPUI ones…</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 url 2022-11-03-CIAT-Library-items.csv | sed 1d | grep -v jspui | sort -u | wc -l
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</span></span><span style="display:flex;"><span>2752
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</span></span></code></pre></div><ul>
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<li>I’m not sure how we’ll handle the duplicates because many items are book chapters or something where they share a PDF</li>
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</ul>
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<h2 id="2022-11-04">2022-11-04</h2>
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<ul>
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<li>I decided to check for old pre-ImageMagick thumbnails on CGSpace by finding any bitstreams with the description “Generated Thumbnail”:</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>localhost/dspacetest= ☘ \COPY (SELECT ds6_bitstream2itemhandle(dspace_object_id) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND text_value='Generated Thumbnail') to /tmp/old-thumbnails.txt;
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</span></span><span style="display:flex;"><span>COPY 1147
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</span></span><span style="display:flex;"><span>$ grep -v <span style="color:#e6db74">'\\N'</span> /tmp/old-thumbnails.txt > /tmp/old-thumbnail-handles.txt
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</span></span><span style="display:flex;"><span>$ wc -l /tmp/old-thumbnail-handles.txt
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</span></span><span style="display:flex;"><span>987 /tmp/old-thumbnail-handles.txt
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</span></span></code></pre></div><ul>
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<li>A bunch of these have <code>\N</code> for some reason when I use the <code>ds6_bitstream2itemhandle</code> function to get their handles so I had to exclude those…
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<ul>
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<li>I forced the media-filter for these items on CGSpace:</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>$ <span style="color:#66d9ef">while</span> read -r handle; <span style="color:#66d9ef">do</span> JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Xmx512m -Dfile.encoding=UTF-8"</span> dspace filter-media -p <span style="color:#e6db74">"ImageMagick PDF Thumbnail"</span> -i $handle -f -v; <span style="color:#66d9ef">done</span> < /tmp/old-thumbnail-handles.txt
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</span></span></code></pre></div><ul>
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<li>Upload some batch records via CSV for Peter</li>
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<li>Update the about page on CGSpace with new text from Peter</li>
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<li>Add a few more ORCID identifiers and names to my growing file <code>2022-09-22-add-orcids.csv</code>
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<ul>
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<li>I tagged fifty-four new authors using this list</li>
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</ul>
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</li>
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<li>I deleted and mapped one duplicate item for Maria Garruccio</li>
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<li>I updated the CG Core website from Bootstrap v4.6 to v5.2</li>
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</ul>
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<h2 id="2022-11-07">2022-11-07</h2>
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<ul>
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<li>I did a harvest on AReS last night but it seems that MELSpace’s sitemap is broken again because we have 10,000 fewer records</li>
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<li>I filed <a href="https://github.com/ecrmnn/iso-3166-1/issues/10">an issue</a> on the iso-3166-1 npm package to update the name of Turkey to Türkiye
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<ul>
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<li>I also filed <a href="https://github.com/flyingcircusio/pycountry/issues/148">an issue</a> and <a href="https://github.com/flyingcircusio/pycountry/pull/149">a pull request</a> on the pycountry package</li>
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<li>I also filed <a href="https://github.com/konstantinstadler/country_converter/issues/121">an issue</a> and <a href="https://github.com/konstantinstadler/country_converter/pull/122">a pull request</a> on the country-converter package</li>
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<li>I also changed one item on CGSpace that had been submitted since the name was changed</li>
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<li>I also imported the new iso-codes 4.12.0 into cgspace-java-helpers</li>
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<li>I also updated it in the DSpace <code>input-forms.xml</code></li>
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<li>I also forked the iso-3166-1 package from npm and updated Swaziland, Macedonia, and Turkey in my fork
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<ul>
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<li>I submitted a <a href="https://github.com/ecrmnn/iso-3166-1/pull/11">pull request</a> to update this upstream</li>
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</ul>
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</li>
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</ul>
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</li>
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<li>Since I was making all these pull requests I also made <a href="https://github.com/konstantinstadler/country_converter/pull/123">one on country-converter for the UN M.49 region “South-eastern Asia”</a></li>
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<li>Port the <a href="https://github.com/DSpace/DSpace/pull/8550">ImageMagick PDF cropbox fix</a> to DSpace 6.x
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<ul>
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<li>I deployed it on CGSpace, ran all updates, and rebooted the host</li>
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<li>I ran the filter-media script on one large collection where many of these PDFs with cropbox issues exist:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Xmx1024m -Dfile.encoding=UTF-8"</span> dspace filter-media -p <span style="color:#e6db74">"ImageMagick PDF Thumbnail"</span> -v -f -i 10568/78 >& /tmp/filter-media-cropbox.log
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</span></span></code></pre></div><ul>
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<li>But looking at the items it processed, I’m not sure it’s working as expected</li>
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</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2022-11/">November, 2022</a></li>
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<li><a href="/cgspace-notes/2022-10/">October, 2022</a></li>
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<li><a href="/cgspace-notes/2022-09/">September, 2022</a></li>
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<li><a href="/cgspace-notes/2022-08/">August, 2022</a></li>
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<li><a href="/cgspace-notes/2022-07/">July, 2022</a></li>
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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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