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Work on CGSpace duplicate DOIs more
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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/2024-04/">April, 2024</a></h2>
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<time datetime="2024-04-04T10:23:00+03:00">Thu Apr 04, 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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<h2 id="2024-04-04">2024-04-04</h2>
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<ul>
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<li>Work on CGSpace duplicate DOIs more</li>
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</ul>
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<h2 id="2024-04-08">2024-04-08</h2>
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<ul>
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<li>Start working on IFPRI’s 2022 batch import
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<ul>
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<li>I ran the duplicate checker against CGSpace and started downloading all linked PDFs</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-04-09">2024-04-09</h2>
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<ul>
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<li>Continue working on IFPRI’s 2022 batch import
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<ul>
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<li>I started validating the potential duplicates in OpenRefine</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-04-12">2024-04-12</h2>
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<ul>
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<li>Finish working on the 650 IFPRI 2022 records that were not already on CGSpace, then uploaded them
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<ul>
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<li>I need to merge the metadata for the remaining 212 that are already on CGSpace</li>
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</ul>
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</li>
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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="2024-04-13">2024-04-13</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="2024-04-14">2024-04-14</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="2024-04-15">2024-04-15</h2>
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<ul>
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<li>Spend some time looking at duplicate DOIs again…</li>
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<li>Delete ~260 duplicate metadata values using the elaborate SQL and sort method I documented here: <a href="https://github.com/DSpace/DSpace/issues/8253#issuecomment-1331756418">https://github.com/DSpace/DSpace/issues/8253#issuecomment-1331756418</a></li>
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<li>Tony noticed that the DSpace 7 REST API is very slow with the embeds so I profiled a bit:</li>
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</ul>
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<pre tabindex="0"><code>$ time curl -s -o /dev/null 'https://cgspace.cgiar.org/server/api/discover/search/objects?query=cg.identifier.project%3AIFPRI*&scope=8f1e9650-fe87-4e6e-889a-1cacfb747408&page=0&size=100&embed=thumbnail,bundles/bitstreams&sort=dcterms.issued,desc'
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curl -s -o /dev/null 0.01s user 0.01s system 0% cpu 47.515 total
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$ time curl -s -o /dev/null 'https://cgspace.cgiar.org/server/api/discover/search/objects?query=cg.identifier.project%3AIFPRI*&scope=8f1e9650-fe87-4e6e-889a-1cacfb747408&page=0&size=100&sort=dcterms.issued,desc'
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curl -s -o /dev/null 0.01s user 0.01s system 0% cpu 4.764 total
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</code></pre><ul>
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<li>Finalize processing the remaining 206 items from the IFPRI 2022 batch set that already existed on CGSpace
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<ul>
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<li>I merged metadata with the existing items</li>
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<li>There are still six remaining items that I identified as being duplicates (3x2) in the IFPRI set itself</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-04-16">2024-04-16</h2>
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<ul>
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<li>Spend some time looking at duplicate DOIs again…</li>
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<li>Assist Deborah with an advanced query on CGSpace for biodiversity and health:</li>
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</ul>
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<pre tabindex="0"><code>dcterms.issued:[2010 TO 2024] AND dcterms.type:"Journal Article" AND (dc.title:"biodiversity" OR dcterms.subject:"biodiversity" OR dc.title:"health" OR dcterms.subject:"health")
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</code></pre><ul>
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<li>Remove CIMMYT URLs and citations from 277 journal articles on CGSpace since it is a bit tacky
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<ul>
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<li>I used this Jython expression in OpenRefine with <a href="https://citation.crosscite.org/docs.html">Crossref’s content negotiation</a> to get citations for all DOIs:</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> urllib2
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span>doi <span style="color:#f92672">=</span> cells[<span style="color:#e6db74">'cg.identifier.doi[en_US]'</span>]<span style="color:#f92672">.</span>value
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</span></span><span style="display:flex;"><span>url <span style="color:#f92672">=</span> <span style="color:#e6db74">"https://api.crossref.org/works/"</span> <span style="color:#f92672">+</span> doi <span style="color:#f92672">+</span> <span style="color:#e6db74">"/transform/text/x-bibliography"</span>
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</span></span><span style="display:flex;"><span>useragent <span style="color:#f92672">=</span> <span style="color:#e6db74">"Python (mailto:a.o@cgiar.org)"</span>
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span>request <span style="color:#f92672">=</span> urllib2<span style="color:#f92672">.</span>Request(url<span style="color:#f92672">.</span>encode(<span style="color:#e6db74">"utf-8"</span>), headers<span style="color:#f92672">=</span>{<span style="color:#e6db74">"User-Agent"</span> : useragent})
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</span></span><span style="display:flex;"><span>get <span style="color:#f92672">=</span> urllib2<span style="color:#f92672">.</span>urlopen(request)
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> get<span style="color:#f92672">.</span>read()<span style="color:#f92672">.</span>decode(<span style="color:#e6db74">'utf-8'</span>)
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</span></span></code></pre></div><ul>
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<li>It took ten or so minutes for it to finish (and note this is Python 2 inside OpenRefine so I had to be careful with Unicode), but worked well!</li>
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</ul>
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<h2 id="2024-04-18">2024-04-18</h2>
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<ul>
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<li>Write a SQL query to build the IFPRI CONTENTdm redirects to Handles:</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> m.text_value, h.handle <span style="color:#66d9ef">FROM</span> metadatavalue m <span style="color:#66d9ef">JOIN</span> handle h <span style="color:#66d9ef">on</span> m.dspace_object_id <span style="color:#f92672">=</span> h.resource_id <span style="color:#66d9ef">WHERE</span> m.metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">28</span> <span style="color:#66d9ef">AND</span> m.text_value <span style="color:#66d9ef">LIKE</span> <span style="color:#e6db74">'Original URL%'</span> <span style="color:#66d9ef">AND</span> h.resource_type_id<span style="color:#f92672">=</span><span style="color:#ae81ff">2</span>;
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</span></span></code></pre></div><ul>
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<li>Similarly, I need a SQL query to get the redirects for duplicate Handles, querying for <code>dcterms.replaces</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><span style="color:#66d9ef">SELECT</span> m.text_value <span style="color:#66d9ef">AS</span> handle_from, h.handle <span style="color:#66d9ef">AS</span> handle_to <span style="color:#66d9ef">FROM</span> metadatavalue m <span style="color:#66d9ef">JOIN</span> handle h <span style="color:#66d9ef">on</span> m.dspace_object_id <span style="color:#f92672">=</span> h.resource_id <span style="color:#66d9ef">WHERE</span> m.metadata_field_id<span style="color:#f92672">=</span><span style="color:#ae81ff">181</span> <span style="color:#66d9ef">AND</span> h.resource_type_id<span style="color:#f92672">=</span><span style="color:#ae81ff">2</span>;
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</span></span></code></pre></div><ul>
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<li>Then I can work that list into an nginx map with redirect, for example:</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>server {
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</span></span><span style="display:flex;"><span>...
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span> if ($new_uri) {
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</span></span><span style="display:flex;"><span> return 301 $new_uri;
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</span></span><span style="display:flex;"><span> }
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</span></span><span style="display:flex;"><span>}
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>map $request_uri $new_uri {
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</span></span><span style="display:flex;"><span> /handle/10568/112821 /handle/10568/97605;
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</span></span><span style="display:flex;"><span>}
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</span></span></code></pre></div><h2 id="2024-04-19">2024-04-19</h2>
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<ul>
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<li>Spend some time looking at duplicate DOIs again…</li>
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<li>Refresh ORCID identifiers from ORCID API and update CGSpace metadata and controlled vocabulary</li>
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</ul>
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<h2 id="2024-04-20">2024-04-20</h2>
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<ul>
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<li>I read an <a href="https://github.com/greenelab/scihub/issues/9">interesting thread about DOI casing</a>
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<ul>
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<li>Apparently the DOI specification says ASCII characters in DOIs are case insensitive</li>
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<li>Indeed, <a href="https://www.crossref.org/documentation/member-setup/constructing-your-dois/">Crossref recommends lower case</a> for all DOIs</li>
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<li>I was curious about the DOIs in our database so I checked before and after lower casing:</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/dspace7= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=220 AND text_value IS NOT NULL AND text_value !='') TO /tmp/dois-sql-before.txt;
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</span></span><span style="display:flex;"><span>COPY 25675
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</span></span><span style="display:flex;"><span>localhost/dspace7= ☘ \COPY (SELECT DISTINCT(lower(text_value)) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=220 AND text_value IS NOT NULL AND text_value !='') TO /tmp/dois-sql-after.txt;
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</span></span><span style="display:flex;"><span>COPY 25666
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</span></span></code></pre></div><ul>
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<li>I need to investigate options for lower casing these in the repository, for example in a curation task, and in all workflows around DSpace metadata…</li>
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</ul>
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<h2 id="2024-04-23">2024-04-23</h2>
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<ul>
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<li>Spent some time writing a Java curation task to normalize DOIs in items when they enter the workflow edit step
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<ul>
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<li>The workflow curation tasks are not documented very well but I got a basic configuration working</li>
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<li>I found a bug in DSpace curation tasks and discussed on Slack</li>
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<li>I finalized the <code>NormalizeDOIs</code> curation task and released v7.6.1.1 of the <a href="https://github.com/ilri/cgspace-java-helpers">cgspace-java-helpers</a> project</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-04-24">2024-04-24</h2>
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<ul>
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<li>A bit more testing of the curation tasks
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<ul>
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<li>I tested a patch by Mark Wood</li>
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</ul>
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</li>
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<li>I added support for normalizing DOIs to this same format to my <a href="https://github.com/ilri/csv-metadata-quality">csv-metadata-quality</a> project</li>
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</ul>
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<h2 id="2024-04-25">2024-04-25</h2>
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<ul>
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<li>I lowercased the remaining 3,900 DOIs on CGSpace that had uppercase ASCII characters</li>
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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="2024-04-26">2024-04-26</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="2024-04-29">2024-04-29</h2>
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<ul>
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<li>Start working on the IFPRI 2020–2021 batch migration
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<ul>
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<li>I modified my <code>check_duplicates.py</code> script to check for DOIs instead of titles, and use a similarity of 1.0 to make sure the match is exact</li>
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</ul>
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</li>
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<li>I noticed something in the Tomcat log:</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>tomcat9[690]: WARNING: The HTTP response header [Content-Disposition] with value [attachment; filename="Literature review on Women’s Empowerment and their Resilience2.pdf"] has been removed from the response because it is invalid
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</span></span><span style="display:flex;"><span>tomcat9[690]: java.lang.IllegalArgumentException: The Unicode character [’] at code point [8,217] cannot be encoded as it is outside the permitted range of 0 to 255
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</span></span></code></pre></div><ul>
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<li>I found the bitstream’s ID and then used the <code>ds6_bitstream2itemhandle</code> <a href="https://wiki.lyrasis.org/display/DSPACE/Helper+SQL+functions+for+DSpace+6">SQL helper function</a> to find the item’s handle
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<ul>
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<li>Then I replaced the curly quote with a regular quote in all bistreams</li>
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</ul>
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</li>
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</ul>
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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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||
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||
<li><a href="/cgspace-notes/2024-10/">October, 2024</a></li>
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||
<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
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<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
|
||
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||
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
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<li><a href="/cgspace-notes/2024-06/">June, 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">
|
||
|
||
<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>
|
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|
||
</aside>
|
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<footer class="blog-footer">
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<p dir="auto">
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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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<p>
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<a href="#">Back to top</a>
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