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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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<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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<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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<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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</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><h2 id="2024-05-15">2024-05-15</h2>
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<ul>
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<li>I got journal titles for 2,900 journal articles that were missing them from Crossref</li>
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</ul>
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<h2 id="2024-05-16">2024-05-16</h2>
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<p>Helping IFPRI with some DSpace 7 API support, these are two queries for items issued in 2024:</p>
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<ul>
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<li><a href="https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued:2024">https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued:2024</a></li>
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<li><a href="https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued_dt%3A%5B2024-01-01T00%3A00%3A00Z%20TO%20%2A%5D">https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued_dt%3A%5B2024-01-01T00%3A00%3A00Z%20TO%20%2A%5D</a> — note the Lucene search syntax is URL encoded version of <code>:[2024-01-01T00:00:00Z TO *]</code></li>
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</ul>
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<p>Both of them return the same number of results and seem identitical as far as I can see, but the second one uses Solr date indexes and requires the full Lucene datetime and range syntax</p>
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<p>I wrote a new version of the <code>check_duplicates.py</code> script to help identify duplicates with different types</p>
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<ul>
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<li>Initially I called it <code>check_duplicates_fast.py</code> but it’s actually not faster</li>
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<li>I need to find a way to deal with duplicates from IFPRI’s repository because there are some mismatched types…</li>
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</ul>
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<h2 id="2024-05-20">2024-05-20</h2>
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<p>Continue working through alternative duplicate matching for IFPRI</p>
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<ul>
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<li>Their item types are sometimes different than ours…</li>
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<li>One thing I think I can say for sure is that the default similarity factor in my script is 0.6, and I rarely see legitimate duplicates with such similarity so I might increase this to 0.7 to reduce the number of items I have to check</li>
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<li>Also, the difference in issue dates is currently 365, but I should reduce that a bit, perhaps to 270 days (9 months)</li>
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</ul>
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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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