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8
docs/categories/index.html
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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -84,7 +84,7 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/categories/notes/">Notes</a></h2>
<p class="blog-post-meta"><time datetime="2024-04-04T10:23:00+03:00">Thu Apr 04, 2024</time> by Alan Orth</p>
<p class="blog-post-meta"><time datetime="2024-05-01T10:39:00+03:00">Wed May 01, 2024</time> by Alan Orth</p>
</header>
<a href='https://alanorth.github.io/cgspace-notes/categories/notes/'>Read more →</a>
@ -108,6 +108,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -116,8 +118,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

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@ -6,7 +6,7 @@
<description>Recent content in Categories on CGSpace Notes</description>
<generator>Hugo</generator>
<language>en-us</language>
<lastBuildDate>Sat, 27 Apr 2024 11:22:58 +0300</lastBuildDate>
<lastBuildDate>Wed, 01 May 2024 10:39:00 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>Notes</title>

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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,31 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-05/">May, 2024</a></h2>
<p class="blog-post-meta"><time datetime="2024-05-01T10:39:00+03:00">Wed May 01, 2024</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2024-05-01">2024-05-01</h2>
<ul>
<li>I dumped all the CGSpace DOIs and resolved them with my <code>crossref_doi_lookup.py</code> script
<ul>
<li>Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2024-05/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-04/">April, 2024</a></h2>
@ -301,24 +326,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-07/">July, 2023</a></h2>
<p class="blog-post-meta"><time datetime="2023-07-01T17:14:36+03:00">Sat Jul 01, 2023</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
2023-07-01 Export CGSpace to check for missing Initiative collection mappings Start harvesting on AReS 2023-07-02 Minor edits to the crossref_doi_lookup.py script while running some checks from 22,000 CGSpace DOIs 2023-07-03 I analyzed the licenses declared by Crossref and found with high confidence that ~400 of ours were incorrect I took the more accurate ones from Crossref and updated the items on CGSpace I took a few hundred ISBNs as well for where we were missing them I also tagged ~4,700 items with missing licenses as &ldquo;Copyrighted; all rights reserved&rdquo; based on their Crossref license status being TDM, mostly from Elsevier, Wiley, and Springer Checking a dozen or so manually, I confirmed that if Crossref only has a TDM license then it&rsquo;s usually copyrighted (could still be open access, but we can&rsquo;t tell via Crossref) I would be curious to write a script to check the Unpaywall API for open access status&hellip; In the past I found that their license status was not very accurate, but the open access status might be more reliable More minor work on the DSpace 7 item views I learned some new Angular template syntax I created a custom component to show Creative Commons licenses on the simple item page I also decided that I don&rsquo;t like the Impact Area icons as a component because they don&rsquo;t have any visual meaning 2023-07-04 Focus group meeting with CGSpace partners about DSpace 7 I added a themed file selection component to the CGSpace theme It displays the bistream description instead of the file name, just like we did in DSpace 6 XMLUI I added a custom component to show share icons 2023-07-05 I spent some time trying to update OpenRXV from Angular 9 to 10 to 11 to 12 to 13 Most things work but there are some minor bugs it seems Mishell from CIP emailed me to say she was having problems approving an item on CGSpace Looking at PostgreSQL I saw there were a dozen or so locks that were several hours and even over one day old so I killed those processes and told her to try again 2023-07-06 Types meeting I wrote a Python script to check Unpaywall for some information about DOIs 2023-07-7 Continue exploring Unpaywall data for some of our DOIs In the past I&rsquo;ve found their licensing information to not be very reliable (preferring Crossref), but I think their open access status is more reliable, especially when the provider is listed as being the publisher Even so, sometimes the version can be &ldquo;acceptedVersion&rdquo;, which is presumably the author&rsquo;s version, as opposed to the &ldquo;publishedVersion&rdquo;, which means it&rsquo;s available as open access on the publisher&rsquo;s website I did some quality assurance and found ~100 that were marked as Limited Access, but should have been Open Access, and fixed a handful of licenses Delete duplicate metadata as described in my DSpace issue from last year: https://github.
<a href='https://alanorth.github.io/cgspace-notes/2023-07/'>Read more →</a>
</article>
<nav class="blog-pagination">
@ -343,6 +350,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -351,8 +360,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

9
docs/categories/notes/index.xml
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@ -6,8 +6,15 @@
<description>Recent content in Notes on CGSpace Notes</description>
<generator>Hugo</generator>
<language>en-us</language>
<lastBuildDate>Sat, 27 Apr 2024 11:22:58 +0300</lastBuildDate>
<lastBuildDate>Wed, 01 May 2024 10:39:00 +0300</lastBuildDate>
<atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>May, 2024</title>
<link>https://alanorth.github.io/cgspace-notes/2024-05/</link>
<pubDate>Wed, 01 May 2024 10:39:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2024-05/</guid>
<description>&lt;h2 id=&#34;2024-05-01&#34;&gt;2024-05-01&lt;/h2&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I dumped all the CGSpace DOIs and resolved them with my &lt;code&gt;crossref_doi_lookup.py&lt;/code&gt; script&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;</description>
</item>
<item>
<title>April, 2024</title>
<link>https://alanorth.github.io/cgspace-notes/2024-04/</link>

56
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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,24 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-07/">July, 2023</a></h2>
<p class="blog-post-meta"><time datetime="2023-07-01T17:14:36+03:00">Sat Jul 01, 2023</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
2023-07-01 Export CGSpace to check for missing Initiative collection mappings Start harvesting on AReS 2023-07-02 Minor edits to the crossref_doi_lookup.py script while running some checks from 22,000 CGSpace DOIs 2023-07-03 I analyzed the licenses declared by Crossref and found with high confidence that ~400 of ours were incorrect I took the more accurate ones from Crossref and updated the items on CGSpace I took a few hundred ISBNs as well for where we were missing them I also tagged ~4,700 items with missing licenses as &ldquo;Copyrighted; all rights reserved&rdquo; based on their Crossref license status being TDM, mostly from Elsevier, Wiley, and Springer Checking a dozen or so manually, I confirmed that if Crossref only has a TDM license then it&rsquo;s usually copyrighted (could still be open access, but we can&rsquo;t tell via Crossref) I would be curious to write a script to check the Unpaywall API for open access status&hellip; In the past I found that their license status was not very accurate, but the open access status might be more reliable More minor work on the DSpace 7 item views I learned some new Angular template syntax I created a custom component to show Creative Commons licenses on the simple item page I also decided that I don&rsquo;t like the Impact Area icons as a component because they don&rsquo;t have any visual meaning 2023-07-04 Focus group meeting with CGSpace partners about DSpace 7 I added a themed file selection component to the CGSpace theme It displays the bistream description instead of the file name, just like we did in DSpace 6 XMLUI I added a custom component to show share icons 2023-07-05 I spent some time trying to update OpenRXV from Angular 9 to 10 to 11 to 12 to 13 Most things work but there are some minor bugs it seems Mishell from CIP emailed me to say she was having problems approving an item on CGSpace Looking at PostgreSQL I saw there were a dozen or so locks that were several hours and even over one day old so I killed those processes and told her to try again 2023-07-06 Types meeting I wrote a Python script to check Unpaywall for some information about DOIs 2023-07-7 Continue exploring Unpaywall data for some of our DOIs In the past I&rsquo;ve found their licensing information to not be very reliable (preferring Crossref), but I think their open access status is more reliable, especially when the provider is listed as being the publisher Even so, sometimes the version can be &ldquo;acceptedVersion&rdquo;, which is presumably the author&rsquo;s version, as opposed to the &ldquo;publishedVersion&rdquo;, which means it&rsquo;s available as open access on the publisher&rsquo;s website I did some quality assurance and found ~100 that were marked as Limited Access, but should have been Open Access, and fixed a handful of licenses Delete duplicate metadata as described in my DSpace issue from last year: https://github.
<a href='https://alanorth.github.io/cgspace-notes/2023-07/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-06/">June, 2023</a></h2>
@ -329,38 +347,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-09/">September, 2022</a></h2>
<p class="blog-post-meta"><time datetime="2022-09-01T09:41:36+03:00">Thu Sep 01, 2022</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2022-09-01">2022-09-01</h2>
<ul>
<li>A bit of work on the &ldquo;Mapping CG Core–CGSpace–MEL–MARLO Types&rdquo; spreadsheet</li>
<li>I tested an item submission on DSpace Test with the Cocoon <code>org.apache.cocoon.uploads.autosave=false</code> change
<ul>
<li>The submission works as expected</li>
</ul>
</li>
<li>Start debugging some region-related issues with csv-metadata-quality
<ul>
<li>I created a new test file <code>test-geography.csv</code> with some different scenarios</li>
<li>I also fixed a few bugs and improved the region-matching logic</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2022-09/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/" rel="prev" role="button">Previous page</a>
@ -385,6 +371,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -393,8 +381,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

63
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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,38 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-09/">September, 2022</a></h2>
<p class="blog-post-meta"><time datetime="2022-09-01T09:41:36+03:00">Thu Sep 01, 2022</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2022-09-01">2022-09-01</h2>
<ul>
<li>A bit of work on the &ldquo;Mapping CG Core–CGSpace–MEL–MARLO Types&rdquo; spreadsheet</li>
<li>I tested an item submission on DSpace Test with the Cocoon <code>org.apache.cocoon.uploads.autosave=false</code> change
<ul>
<li>The submission works as expected</li>
</ul>
</li>
<li>Start debugging some region-related issues with csv-metadata-quality
<ul>
<li>I created a new test file <code>test-geography.csv</code> with some different scenarios</li>
<li>I also fixed a few bugs and improved the region-matching logic</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2022-09/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-08/">August, 2022</a></h2>
@ -324,31 +356,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-11/">November, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-11-02T22:27:07+02:00">Tue Nov 02, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-11-02">2021-11-02</h2>
<ul>
<li>I experimented with manually sharding the Solr statistics on DSpace Test</li>
<li>First I exported all the 2019 stats from CGSpace:</li>
</ul>
<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>$ ./run.sh -s http://localhost:8081/solr/statistics -f <span style="color:#e6db74">&#39;time:2019-*&#39;</span> -a export -o statistics-2019.json -k uid
</span></span><span style="display:flex;"><span>$ zstd statistics-2019.json
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-11/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/2/" rel="prev" role="button">Previous page</a>
@ -373,6 +380,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -381,8 +390,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

70
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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,31 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-11/">November, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-11-02T22:27:07+02:00">Tue Nov 02, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-11-02">2021-11-02</h2>
<ul>
<li>I experimented with manually sharding the Solr statistics on DSpace Test</li>
<li>First I exported all the 2019 stats from CGSpace:</li>
</ul>
<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>$ ./run.sh -s http://localhost:8081/solr/statistics -f <span style="color:#e6db74">&#39;time:2019-*&#39;</span> -a export -o statistics-2019.json -k uid
</span></span><span style="display:flex;"><span>$ zstd statistics-2019.json
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-10/">October, 2021</a></h2>
@ -326,45 +351,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-02-01T10:13:54+02:00">Mon Feb 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-02-01">2021-02-01</h2>
<ul>
<li>Abenet said that CIP found more duplicate records in their export from AReS
<ul>
<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>
<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>
</ul>
</li>
<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
<li>Check the results of the AReS harvesting from last night:</li>
</ul>
<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">&#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#39;</span>
</span></span><span style="display:flex;"><span>{
</span></span><span style="display:flex;"><span> &#34;count&#34; : 100875,
</span></span><span style="display:flex;"><span> &#34;_shards&#34; : {
</span></span><span style="display:flex;"><span> &#34;total&#34; : 1,
</span></span><span style="display:flex;"><span> &#34;successful&#34; : 1,
</span></span><span style="display:flex;"><span> &#34;skipped&#34; : 0,
</span></span><span style="display:flex;"><span> &#34;failed&#34; : 0
</span></span><span style="display:flex;"><span> }
</span></span><span style="display:flex;"><span>}
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-02/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/3/" rel="prev" role="button">Previous page</a>
@ -389,6 +375,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -397,8 +385,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

71
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@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,45 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-02/">February, 2021</a></h2>
<p class="blog-post-meta"><time datetime="2021-02-01T10:13:54+02:00">Mon Feb 01, 2021</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2021-02-01">2021-02-01</h2>
<ul>
<li>Abenet said that CIP found more duplicate records in their export from AReS
<ul>
<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>
<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>
</ul>
</li>
<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
<li>Check the results of the AReS harvesting from last night:</li>
</ul>
<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">&#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#39;</span>
</span></span><span style="display:flex;"><span>{
</span></span><span style="display:flex;"><span> &#34;count&#34; : 100875,
</span></span><span style="display:flex;"><span> &#34;_shards&#34; : {
</span></span><span style="display:flex;"><span> &#34;total&#34; : 1,
</span></span><span style="display:flex;"><span> &#34;successful&#34; : 1,
</span></span><span style="display:flex;"><span> &#34;skipped&#34; : 0,
</span></span><span style="display:flex;"><span> &#34;failed&#34; : 0
</span></span><span style="display:flex;"><span> }
</span></span><span style="display:flex;"><span>}
</span></span></code></pre></div>
<a href='https://alanorth.github.io/cgspace-notes/2021-02/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-01/">January, 2021</a></h2>
@ -332,32 +371,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-05-02">2020-05-02</h2>
<ul>
<li>Peter said that CTA is having problems submitting an item to CGSpace
<ul>
<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in &lsquo;idle in transaction&rsquo; and &lsquo;waiting for lock&rsquo; state are increasing again</li>
<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-05/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/4/" rel="prev" role="button">Previous page</a>
@ -382,6 +395,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -390,8 +405,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

60
docs/categories/notes/page/6/index.html
View File

@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,32 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-05-02">2020-05-02</h2>
<ul>
<li>Peter said that CTA is having problems submitting an item to CGSpace
<ul>
<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in &lsquo;idle in transaction&rsquo; and &lsquo;waiting for lock&rsquo; state are increasing again</li>
<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-05/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-04/">April, 2020</a></h2>
@ -373,34 +399,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-07/">July, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-07-01T12:13:51+03:00">Mon Jul 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-07-01">2019-07-01</h2>
<ul>
<li>Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice</li>
<li>Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
<ul>
<li><a href="https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">DSpace Test</a></li>
<li><a href="https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">CGSpace</a></li>
</ul>
</li>
<li>Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-07/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/5/" rel="prev" role="button">Previous page</a>
@ -425,6 +423,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -433,8 +433,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

58
docs/categories/notes/page/7/index.html
View File

@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,34 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-07/">July, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-07-01T12:13:51+03:00">Mon Jul 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-07-01">2019-07-01</h2>
<ul>
<li>Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice</li>
<li>Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
<ul>
<li><a href="https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">DSpace Test</a></li>
<li><a href="https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">CGSpace</a></li>
</ul>
</li>
<li>Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2019-07/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-06/">June, 2019</a></h2>
@ -367,30 +395,6 @@ sys 0m1.979s
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-09/">September, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-09-02T09:55:54+03:00">Sun Sep 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-09-02">2018-09-02</h2>
<ul>
<li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li>
<li>I&rsquo;ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
<li>Also, I&rsquo;ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
<li>I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-09/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/6/" rel="prev" role="button">Previous page</a>
@ -415,6 +419,8 @@ sys 0m1.979s
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -423,8 +429,6 @@ sys 0m1.979s
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

63
docs/categories/notes/page/8/index.html
View File

@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,30 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-09/">September, 2018</a></h2>
<p class="blog-post-meta"><time datetime="2018-09-02T09:55:54+03:00">Sun Sep 02, 2018</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2018-09-02">2018-09-02</h2>
<ul>
<li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li>
<li>I&rsquo;ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
<li>Also, I&rsquo;ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
<li>I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-09/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-08/">August, 2018</a></h2>
@ -380,39 +404,6 @@ dspace.log.2018-01-02:34
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-11-01">2017-11-01</h2>
<ul>
<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
</ul>
<h2 id="2017-11-02">2017-11-02</h2>
<ul>
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
</ul>
<pre tabindex="0"><code># grep -c &#34;CORE&#34; /var/log/nginx/access.log
0
</code></pre><ul>
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
</ul>
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
</article>
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/categories/notes/page/7/" rel="prev" role="button">Previous page</a>
@ -437,6 +428,8 @@ COPY 54701
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -445,8 +438,6 @@ COPY 54701
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>

39
docs/categories/notes/page/9/index.html
View File

@ -10,7 +10,7 @@
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2024-04-27T11:22:58+03:00" />
<meta property="og:updated_time" content="2024-05-01T10:39:00+03:00" />
@ -81,6 +81,39 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2017-11-01">2017-11-01</h2>
<ul>
<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
</ul>
<h2 id="2017-11-02">2017-11-02</h2>
<ul>
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
</ul>
<pre tabindex="0"><code># grep -c &#34;CORE&#34; /var/log/nginx/access.log
0
</code></pre><ul>
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
</ul>
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
@ -150,6 +183,8 @@
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2024-05/">May, 2024</a></li>
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
@ -158,8 +193,6 @@
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
<li><a href="/cgspace-notes/2023-12/">December, 2023</a></li>
</ol>
</section>