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<body>
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<header class="blog-header">
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<div class="container">
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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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</header>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-02-01T10:13:54+02:00">Mon Feb 01, 2021</time> by Alan Orth 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="2021-02-01">2021-02-01</h2>
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<ul>
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<li>Abenet said that CIP found more duplicate records in their export from AReS
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<ul>
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<li>I re-opened <a href="https://github.com/ilri/OpenRXV/issues/67">the issue</a> on OpenRXV where we had previously noticed this</li>
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<li>The shared link where the duplicates are is here: <a href="https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6">https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6</a></li>
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</ul>
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</li>
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<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
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<li>Check the results of the AReS harvesting from last night:</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>$ curl -s <span style="color:#e6db74">'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'</span>
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</span></span><span style="display:flex;"><span>{
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</span></span><span style="display:flex;"><span> "count" : 100875,
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</span></span><span style="display:flex;"><span> "_shards" : {
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</span></span><span style="display:flex;"><span> "total" : 1,
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</span></span><span style="display:flex;"><span> "successful" : 1,
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</span></span><span style="display:flex;"><span> "skipped" : 0,
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</span></span><span style="display:flex;"><span> "failed" : 0
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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></code></pre></div>
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<a href='https://alanorth.github.io/cgspace-notes/2021-02/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-01/">January, 2021</a></h2>
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<p class="blog-post-meta"><time datetime="2021-01-03T10:13:54+02:00">Sun Jan 03, 2021</time> by Alan Orth 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="2021-01-03">2021-01-03</h2>
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<ul>
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<li>Peter notified me that some filters on AReS were broken again
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<ul>
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<li>It’s the same issue with the field names getting <code>.keyword</code> appended to the end that I already <a href="https://github.com/ilri/OpenRXV/issues/66">filed an issue on OpenRXV about last month</a></li>
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<li>I fixed the broken filters (careful to not edit any others, lest they break too!)</li>
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</ul>
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</li>
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<li>Fix an issue with start page number for the DSpace REST API and statistics API in OpenRXV
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<ul>
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<li>The start page had been “1” in the UI, but in the backend they were doing some gymnastics to adjust to the zero-based offset/limit/page of the DSpace REST API and the statistics API</li>
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<li>I adjusted it to default to 0 and added a note to the admin screen</li>
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<li>I realized that this issue was actually causing the first page of 100 statistics to be missing…</li>
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<li>For example, <a href="https://cgspace.cgiar.org/handle/10568/66839">this item</a> has 51 views on CGSpace, but 0 on AReS</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2021-01/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-12/">December, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-12-01T11:32:54+02:00">Tue Dec 01, 2020</time> by Alan Orth 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="2020-12-01">2020-12-01</h2>
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<ul>
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<li>Atmire responded about the issue with duplicate data in our Solr statistics
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<ul>
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<li>They noticed that some records in the statistics-2015 core haven’t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven’t migrated any of the records yet</li>
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<li>That’s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
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<li>I started processing those (about 411,000 records):</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-12/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</a></h2>
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<p class="blog-post-meta"><time datetime="2020-11-15T13:27:35+02:00">Sun Nov 15, 2020</time> by Alan Orth 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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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/migration/" rel="tag">Migration</a>
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</p>
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</header>
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<p>Notes about the DSpace 6 upgrade on CGSpace in 2020-11.</p>
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<a href='https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-11/">November, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-11-01T13:11:54+02:00">Sun Nov 01, 2020</time> by Alan Orth 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="2020-11-01">2020-11-01</h2>
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<ul>
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<li>Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
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<ul>
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<li>So far we’ve spent at least fifty hours to process the statistics and statistics-2019 core… wow.</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-11/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-10/">October, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-10-06T16:55:54+03:00">Tue Oct 06, 2020</time> by Alan Orth 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="2020-10-06">2020-10-06</h2>
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<ul>
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<li>Add tests for the new <code>/items</code> POST handlers to the DSpace 6.x branch of my <a href="https://github.com/ilri/dspace-statistics-api/tree/v6_x">dspace-statistics-api</a>
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<ul>
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<li>It took a bit of extra work because I had to learn how to mock the responses for when Solr is not available</li>
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<li>Tag and release version 1.3.0 on GitHub: <a href="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0">https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0</a></li>
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</ul>
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</li>
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<li>Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
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<ul>
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<li>During the FlywayDB migration I got an error:</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-10/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-09/">September, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-09-02T15:35:54+03:00">Wed Sep 02, 2020</time> by Alan Orth 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="2020-09-02">2020-09-02</h2>
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<ul>
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<li>Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS</li>
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<li>The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
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<ul>
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<li>I restarted it again now and told Moayad that the automatic indexing isn’t working</li>
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</ul>
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</li>
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<li>Add <code>Alliance of Bioversity International and CIAT</code> to affiliations on CGSpace</li>
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<li>Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
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<ul>
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<li>I filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/39">https://github.com/ilri/OpenRXV/issues/39</a></li>
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</ul>
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</li>
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<li>I filed an issue on OpenRXV to make some minor edits to the admin UI: <a href="https://github.com/ilri/OpenRXV/issues/40">https://github.com/ilri/OpenRXV/issues/40</a></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-09/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-08/">August, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-08-02T15:35:54+03:00">Sun Aug 02, 2020</time> by Alan Orth 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="2020-08-02">2020-08-02</h2>
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<ul>
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<li>I spent a few days working on a Java-based curation task to tag items with ISO 3166-1 Alpha2 country codes based on their <code>cg.coverage.country</code> text values
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<ul>
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<li>It looks up the names in ISO 3166-1 first, and then in our CGSpace countries mapping (which has five or so of Peter’s preferred “display” country names)</li>
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<li>It implements a “force” mode too that will clear existing country codes and re-tag everything</li>
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<li>It is class based so I can easily add support for other vocabularies, and the technique could even be used for organizations with mappings to ROR and Clarisa…</li>
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</ul>
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</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-08/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-07/">July, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-07-01T10:53:54+03:00">Wed Jul 01, 2020</time> by Alan Orth 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="2020-07-01">2020-07-01</h2>
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<ul>
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<li>A few users noticed that CGSpace wasn’t loading items today, item pages seem blank
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<ul>
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<li>I looked at the PostgreSQL locks but they don’t seem unusual</li>
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<li>I guess this is the same “blank item page” issue that we had a few times in 2019 that we never solved</li>
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<li>I restarted Tomcat and PostgreSQL and the issue was gone</li>
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</ul>
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</li>
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<li>Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the <code>5_x-prod</code> branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter’s request</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-07/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth 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="2020-06-01">2020-06-01</h2>
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<ul>
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<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
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<ul>
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<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
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</ul>
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</li>
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<li>In other news, I checked the statistics API on DSpace 6 and it’s working</li>
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<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
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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/2022-08/">August, 2022</a></li>
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<li><a href="/cgspace-notes/2022-07/">July, 2022</a></li>
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<li><a href="/cgspace-notes/2022-06/">June, 2022</a></li>
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<li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
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<li><a href="/cgspace-notes/2022-04/">April, 2022</a></li>
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</ol>
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</section>
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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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