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<meta property="og:description" content="2023-06-02
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Spend some time testing my post_bitstreams.py script to update thumbnails for items on CGSpace
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Interestingly I found an item with a JFIF thumbnail and another with a WebP thumbnail…
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Meeting with Valentina, Stefano, and Sara about MODS metadata in CGSpace
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They have experience with improving the MODS interface in MELSpace’s OAI-PMH for use with AGRIS and were curious if we could do the same in CGSpace
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From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then just add a bunch of our fields to the crosswalk
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<meta name="twitter:description" content="2023-06-02
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Spend some time testing my post_bitstreams.py script to update thumbnails for items on CGSpace
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||
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Interestingly I found an item with a JFIF thumbnail and another with a WebP thumbnail…
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Meeting with Valentina, Stefano, and Sara about MODS metadata in CGSpace
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They have experience with improving the MODS interface in MELSpace’s OAI-PMH for use with AGRIS and were curious if we could do the same in CGSpace
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From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then just add a bunch of our fields to the crosswalk
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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/2023-06/">June, 2023</a></h2>
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<time datetime="2023-06-02T10:29:36+03:00">Fri Jun 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="2023-06-02">2023-06-02</h2>
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<ul>
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<li>Spend some time testing my <code>post_bitstreams.py</code> script to update thumbnails for items on CGSpace
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<ul>
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<li>Interestingly I found an item with a JFIF thumbnail and another with a WebP thumbnail…</li>
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||
</ul>
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||
</li>
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<li>Meeting with Valentina, Stefano, and Sara about MODS metadata in CGSpace
|
||
<ul>
|
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<li>They have experience with improving the MODS interface in MELSpace’s OAI-PMH for use with AGRIS and were curious if we could do the same in CGSpace</li>
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<li>From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then just add a bunch of our fields to the crosswalk</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-04">2023-06-04</h2>
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<ul>
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<li>Upgrade CGSpace to Ubuntu 22.04
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<ul>
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<li>The upgrade was mostly normal, but I had to unhold the openjdk package in order for <code>do-release-upgrade</code> to run:</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># apt-mark hold openjdk-8-jdk-headless:amd64 openjdk-8-jre-headless:amd64
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</span></span></code></pre></div><ul>
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<li>In <a href="/cgspace-notes/2022-11/">2022-11</a> an upstream Java update broke the DSpace 6 Handle server so we will have to pin this again after the upgrade to Ubuntu 22.04</li>
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<li>After the upgrade I made sure CGSpace was working, then proceeded to upgrade PostgreSQL from 12 to 14, like I did on <a href="/cgspace-notes/2023-03/">DSpace Test in 2023-03</a></li>
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<li>Then I had to downgrade OpenJDK to fix the Handle server using the ones I had previously downloaded for Ubuntu 20.04 because they no longer exist on Launchpad:</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># dpkg -i openjdk-8-j*8u342-b07*.deb
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</span></span></code></pre></div><ul>
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<li>Export CGSpace to fix missing Initiative collection mappings</li>
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<li>Start a harvest on AReS</li>
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<li>Work on the DSpace 7 migration a bit more
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<ul>
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<li>I decided to rebase and drop all the submission form edits because they conflict every time upstream changes!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-06">2023-06-06</h2>
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<ul>
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<li>Fix some incorrect ORCID identifiers for an Alliance author on CGSpace</li>
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<li>Export our list of ORCID identifiers, resolve them, and update the records in CGSpace:</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>$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml 2022-09-22-add-orcids.csv| grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u > /tmp/2023-06-06-orcids.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/resolve_orcids.py -i /tmp/2023-06-06-orcids.txt -o /tmp/2023-06-06-orcids-names.txt -d
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</span></span><span style="display:flex;"><span>$ ./ilri/update_orcids.py -i /tmp/2023-06-06-orcids-names.txt -db dspacetest -u dspace -p <span style="color:#e6db74">'ffff'</span> -m <span style="color:#ae81ff">247</span>
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</span></span></code></pre></div><ul>
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<li>Start working on updating the MODS schema in CGSpace from 3.1 to 3.8 based on Stefano and Salem’s work last year</li>
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</ul>
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<h2 id="2023-06-08">2023-06-08</h2>
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<ul>
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<li>Continue working on the MODS schema mapping</li>
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<li>Export CGSpace to check and update <code>dcterms.extent</code> fields
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<ul>
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<li>I normalized about 1,500 to use either “p. 1-6” or “5 p.” format</li>
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<li>Also, I used this GREL expression to extract missing pages from the citation field: <code>cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*(pp?\.\s?\d+[-–]\d+).*/)[0]</code></li>
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<li>This was over 4,000 items with a format like “p. 1-6” and “pp. 1-6” in the citation</li>
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<li>I used another GREL expression to extract another 5,000: <code>cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*?(\d+\s+?[Pp]+\.).*/)[0]</code></li>
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<li>This was for the format like “1 p.” (note we had to protect against the greedy <code>.*</code> in the beginning)</li>
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</ul>
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</li>
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<li>I also did some work to capture a handful of missing DOIs and ISSNs, but it was only about 100 items and I will have to wait until the 10,000+ above finish importing</li>
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</ul>
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<h2 id="2023-06-09">2023-06-09</h2>
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<ul>
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<li>I see there are ~200 users in CGSpace that have registered with their CGIAR email address using a password as opposed to using Active 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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">SELECT</span> <span style="color:#f92672">*</span> <span style="color:#66d9ef">FROM</span> eperson <span style="color:#66d9ef">WHERE</span> email <span style="color:#66d9ef">LIKE</span> <span style="color:#e6db74">'%cgiar.org'</span> <span style="color:#66d9ef">AND</span> netid <span style="color:#66d9ef">IS</span> <span style="color:#66d9ef">NOT</span> <span style="color:#66d9ef">NULL</span> <span style="color:#66d9ef">AND</span> password <span style="color:#66d9ef">IS</span> <span style="color:#66d9ef">NOT</span> <span style="color:#66d9ef">NULL</span>;
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</span></span></code></pre></div><ul>
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<li>I am wondering if I should delete their passwords and tell them use log in using LDAP
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<ul>
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<li>As an initial test I will reset a few accounts including my own that have passwords and salts:</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">UPDATE</span> eperson <span style="color:#66d9ef">SET</span> password<span style="color:#f92672">=</span><span style="color:#66d9ef">DEFAULT</span>,salt<span style="color:#f92672">=</span><span style="color:#66d9ef">DEFAULT</span>,digest_algorithm<span style="color:#f92672">=</span><span style="color:#66d9ef">DEFAULT</span> <span style="color:#66d9ef">WHERE</span> netid <span style="color:#66d9ef">IN</span> (<span style="color:#e6db74">'axxxx'</span>, <span style="color:#e6db74">'axxxx'</span>, <span style="color:#e6db74">'bxxxx'</span>);
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</span></span></code></pre></div><ul>
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<li>I also decided to reset passwords/salts for CGIAR accounts that have not been active since 2021 (1.5 years ago):</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-sql" data-lang="sql"><span style="display:flex;"><span><span style="color:#66d9ef">UPDATE</span> eperson <span style="color:#66d9ef">SET</span> password<span style="color:#f92672">=</span><span style="color:#66d9ef">DEFAULT</span>,salt<span style="color:#f92672">=</span><span style="color:#66d9ef">DEFAULT</span>,digest_algorithm<span style="color:#f92672">=</span><span style="color:#66d9ef">DEFAULT</span> <span style="color:#66d9ef">WHERE</span> email <span style="color:#66d9ef">LIKE</span> <span style="color:#e6db74">'%cgiar.org'</span> <span style="color:#66d9ef">AND</span> netid <span style="color:#66d9ef">IS</span> <span style="color:#66d9ef">NOT</span> <span style="color:#66d9ef">NULL</span> <span style="color:#66d9ef">AND</span> password <span style="color:#66d9ef">IS</span> <span style="color:#66d9ef">NOT</span> <span style="color:#66d9ef">NULL</span> <span style="color:#66d9ef">AND</span> salt <span style="color:#66d9ef">IS</span> <span style="color:#66d9ef">NOT</span> <span style="color:#66d9ef">NULL</span> <span style="color:#66d9ef">AND</span> last_active <span style="color:#f92672"><</span> <span style="color:#e6db74">'2022-01-01'</span>::date;
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</span></span></code></pre></div><ul>
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<li>This was about 100 accounts…
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<ul>
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<li>I will wait some more time before I decide what to do about the more current ones</li>
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</ul>
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</li>
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<li>Add a few more ORCID identifiers to my list and tag them on CGSpace</li>
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</ul>
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<h2 id="2023-06-10">2023-06-10</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative mappings
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<ul>
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<li>Start a harvest on AReS</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-11">2023-06-11</h2>
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<ul>
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<li>File <a href="https://github.com/DSpace/DSpace/issues/8900">an issue</a> on DSpace for the <code>Content-Disposition</code> bug causing images to get downloaded instead of opened inline</li>
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</ul>
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<h2 id="2023-06-12">2023-06-12</h2>
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<ul>
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<li>Export CGSpace to do some more work extracting volume and issue from citations for items where they are missing
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<ul>
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<li>I found and fixed over 7,000!</li>
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<li>Then I found and extracted another 7,000 items with no extents (pages)</li>
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<li>Then I replaced all occurences of en dashes for ranges in pages with regular hyphens</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-13">2023-06-13</h2>
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<ul>
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<li>Last night I finally figured out how to do basic overrides to the simple item view in Angular</li>
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<li>Add a handful of new ORCID identifiers to my list and tag them on CGSpace</li>
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<li>Extract a list of all the proposed actions for CG Core output types and create a <a href="https://github.com/AgriculturalSemantics/cg-core/issues/45">new issue for them on CG Core’s GitHub repository</a></li>
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<li>Extract a list of all the proposed actions for CG Core output types for MARLO and create <a href="https://github.com/CCAFS/MARLO/issues/2479">a new issue for them on MARLO’s GitHub repository</a></li>
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<li>Meeting with Indira, Ryan, and Abenet to discuss plans for the DSpace 7 focus group</li>
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</ul>
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<h2 id="2023-06-14">2023-06-14</h2>
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<ul>
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<li>Did some more work on the DSpace 7 Test to improve the submission forms and the look and feel</li>
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<li>Extract a list of all the proposed actions for CG Core output types for MEL and create <a href="https://github.com/CodeObia/MEL/issues/11216">a new issue for them on MEL’s GitHub repository</a></li>
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<li>I filed <a href="https://github.com/DSpace/dspace-angular/issues/2309">an issue about the yarn merge-i18n script</a></li>
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<li>I made <a href="https://github.com/DSpace/dspace-angular/pull/2306">a pull request for some Finnish language i18n strings</a></li>
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<li>I made <a href="https://github.com/DSpace/dspace-angular/pull/2306">a pull request to lint the i18n en.json5 file</a></li>
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</ul>
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<h2 id="2023-06-15">2023-06-15</h2>
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<ul>
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<li>A lot more work on DSpace 7
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<ul>
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<li>I tested some pull requests and worked on the style of the item view and homepage</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-16">2023-06-16</h2>
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<ul>
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<li>A lot more work on DSpace 7
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<ul>
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<li>I made <a href="https://github.com/DSpace/dspace-angular/pull/2316">a pull request to adjust font weight in item counts </a></li>
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<li>I made <a href="https://github.com/DSpace/dspace-angular/pull/2317">a pull request to update the ESLint configuration for JSON5</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-06-17">2023-06-17</h2>
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<ul>
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<li>Export CGSpace to check for missing Initiative collection mappings
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<ul>
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<li>I also spent some time doing sanity checks on countries, regions, DOIs, and more</li>
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</ul>
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</li>
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<li>I lowercased all our AGROVOC keywords in <code>dcterms.subject</code>:</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-sql" data-lang="sql"><span style="display:flex;"><span>dspace<span style="color:#f92672">=#</span> <span style="color:#66d9ef">BEGIN</span>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">BEGIN</span>
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</span></span><span style="display:flex;"><span>dspace<span style="color:#f92672">=*#</span> <span style="color:#66d9ef">UPDATE</span> metadatavalue <span style="color:#66d9ef">SET</span> text_value<span style="color:#f92672">=</span><span style="color:#66d9ef">LOWER</span>(text_value) <span style="color:#66d9ef">WHERE</span> dspace_object_id <span style="color:#66d9ef">IN</span> (<span style="color:#66d9ef">SELECT</span> uuid <span style="color:#66d9ef">FROM</span> item) <span style="color:#66d9ef">AND</span> metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">187</span> <span style="color:#66d9ef">AND</span> text_value <span style="color:#f92672">~</span> <span style="color:#e6db74">'[[:upper:]]'</span>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">UPDATE</span> <span style="color:#ae81ff">2392</span>
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</span></span><span style="display:flex;"><span>dspace<span style="color:#f92672">=*#</span> <span style="color:#66d9ef">COMMIT</span>;
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">COMMIT</span>
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</span></span></code></pre></div><ul>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2023-06-19">2023-06-19</h2>
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||
<ul>
|
||
<li>Today I started getting an error on DSpace 7 Test
|
||
<ul>
|
||
<li>The page loads, and then when it is almost done it goes blank to white with this in the console:</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>ERROR DOMException: CSSStyleSheet.cssRules getter: Not allowed to access cross-origin stylesheet
|
||
</span></span></code></pre></div><ul>
|
||
<li>I restarted Angular, but it didn’t fix it</li>
|
||
<li>The <code>yarn test:rest</code> script shows everything OK, and I haven’t changed anything recently…</li>
|
||
<li>I re-compiled the Angular UI using the default theme and it was the same…</li>
|
||
<li>I tried in Firefox Nightly and it works…
|
||
<ul>
|
||
<li>So it must be something related to the browser</li>
|
||
<li>I tried clearing all the session storage / cookies and refreshing and it worked</li>
|
||
</ul>
|
||
</li>
|
||
<li>I switched back to the CGSpace theme and it happened again
|
||
<ul>
|
||
<li>I had a hunch it might be due to the GDPR cookie plugin in my browser, so I disabled that and then refreshed and it worked… hmmm</li>
|
||
</ul>
|
||
</li>
|
||
<li>Upload thumbnails for about 42 IITA Journal Articles after resolving their DOIs and making sure they were not CC ND
|
||
<ul>
|
||
<li>I fixed a few bugs in <code>get_scihub_pdfs.py</code> in the process</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<!-- raw HTML omitted -->
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
</div> <!-- /.blog-main -->
|
||
|
||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2023-06/">June, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-05/">May, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-04/">April, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-03/">March, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-02/">February, 2023</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
</aside>
|
||
|
||
|
||
</div> <!-- /.row -->
|
||
</div> <!-- /.container -->
|
||
|
||
|
||
|
||
<footer class="blog-footer">
|
||
<p dir="auto">
|
||
|
||
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
||
|
||
</p>
|
||
<p>
|
||
<a href="#">Back to top</a>
|
||
</p>
|
||
</footer>
|
||
|
||
|
||
</body>
|
||
|
||
</html>
|