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<meta property="og:title" content="May, 2024" />
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<meta property="og:description" content="2024-05-01
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I dumped all the CGSpace DOIs and resolved them with my crossref_doi_lookup.py script
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Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc
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" />
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<meta name="twitter:title" content="May, 2024"/>
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<meta name="twitter:description" content="2024-05-01
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I dumped all the CGSpace DOIs and resolved them with my crossref_doi_lookup.py script
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Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc
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"/>
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"author": {
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<title>May, 2024 | CGSpace Notes</title>
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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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/2024-05/">May, 2024</a></h2>
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<p class="blog-post-meta">
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<time datetime="2024-05-01T10:39:00+03:00">Wed May 01, 2024</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="2024-05-01">2024-05-01</h2>
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<ul>
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<li>I dumped all the CGSpace DOIs and resolved them with my <code>crossref_doi_lookup.py</code> script
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<ul>
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<li>Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-05-05">2024-05-05</h2>
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<ul>
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<li>Spend some time looking at duplicate DOIs again…</li>
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</ul>
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<h2 id="2024-05-06">2024-05-06</h2>
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<ul>
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<li>Spend some time looking at duplicate DOIs again…</li>
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</ul>
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<h2 id="2024-05-07">2024-05-07</h2>
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<ul>
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<li>Discuss RSS feeds and OpenSearch with IWMI
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<ul>
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<li>It seems our OpenSearch feed settings are using the defaults, so I need to copy some of those over from our old DSpace 6 branch</li>
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</ul>
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</li>
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<li>I saw a patch for an interesting issue on DSpace GitHub: <a href="https://github.com/DSpace/DSpace/issues/9544">Error submitting or deleting items - URI too long when user is in a large number of groups</a>
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<ul>
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<li>I hadn’t realized it, but we have lots of those errors:</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>$ zstdgrep -a <span style="color:#e6db74">'URI Too Long'</span> log/dspace.log-2024-04-* | wc -l
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</span></span><span style="display:flex;"><span>1423
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</span></span></code></pre></div><ul>
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<li>Spend some time looking at duplicate DOIs again…</li>
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</ul>
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<h2 id="2024-05-08">2024-05-08</h2>
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<ul>
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<li>Spend some time looking at duplicate DOIs again…
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<ul>
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<li>I finally finished looking at the duplicate DOIs for journal articles</li>
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<li>I updated the list of handle redirects and there are 386 of them!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-05-09">2024-05-09</h2>
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<ul>
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<li>Spend some time working on the IFPRI 2020–2021 batch
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<ul>
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<li>I started by checking for exact duplicates (1.0 similarity) using DOI, type, and issue date</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-05-12">2024-05-12</h2>
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<ul>
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<li>I couldn’t figure out how to do a complex join on withdrawn items along with their metadata, so I pull out a few like titles, handles, and provenance separately:</li>
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</ul>
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<pre tabindex="0"><code class="language-psql" data-lang="psql">dspace=# \COPY (SELECT i.uuid, m.text_value AS uri FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=25) TO /tmp/withdrawn-handles.csv CSV HEADER;
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dspace=# \COPY (SELECT i.uuid, m.text_value AS title FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=64) TO /tmp/withdrawn-titles.csv CSV HEADER;
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dspace=# \COPY (SELECT i.uuid, m.text_value AS submitted_by FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=28 AND m.text_value LIKE 'Submitted by%') TO /tmp/withdrawn-submitted-by.csv CSV HEADER;
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</code></pre><ul>
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<li>Then joined them:</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>$ csvjoin -c uuid /tmp/withdrawn-title.csv /tmp/withdrawn-handles.csv /tmp/withdrawn-submitted-by.csv > /tmp/withdrawn.csv
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</span></span></code></pre></div><ul>
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<li>This gives me an insight into who submitted at 334 of the duplicates over the past few years…</li>
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<li>I fixed a few hundred titles with leading/trailing whitespace, newlines, and ligatures like ff, fi, fl, ffi, and ffl</li>
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</ul>
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<h2 id="2024-05-13">2024-05-13</h2>
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<ul>
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<li>Export a list of IFPRI information products with handle links and CONTENTdm links:</li>
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</ul>
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<pre tabindex="0"><code>$ csvgrep -c 'dc.description.provenance[en_US]' -m 'CONTENTdm' cgspace.csv \
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| csvcut -c 'id,dc.description.provenance[en_US],dc.identifier.uri[en_US]' \
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| tee /tmp/ifpri-redirects.csv \
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| csvstat --count
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2645
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</code></pre><ul>
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<li>I discovered the <code>/server/api/pid/find</code> endpoint today, which is much more direct and manageable than the <code>/server/api/discover/search/objects?query=</code> endpoint when trying to get metadata for a Handle (item, collection, or community)
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<ul>
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<li>The “pid” stands for permanent identifiers apparently, and we can use it like this:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>https://dspace7test.ilri.org/server/api/pid/find?id=10568/118424
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</code></pre><!-- raw HTML omitted -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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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/2024-05/">May, 2024</a></li>
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<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
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<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
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<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
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<li><a href="/cgspace-notes/2024-01/">January, 2024</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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</ol>
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</section>
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</aside>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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