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<meta property="og:title" content="June, 2023" />
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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:title" content="June, 2023"/>
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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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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
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<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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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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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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<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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<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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