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Add notes for 2022-09-29

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Alan Orth
2022-09-28 17:10:23 +03:00
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@ -25,7 +25,7 @@ I also fixed a few bugs and improved the region-matching logic
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-09/" />
<meta property="article:published_time" content="2022-09-01T09:41:36+03:00" />
<meta property="article:modified_time" content="2022-09-25T21:02:46+03:00" />
<meta property="article:modified_time" content="2022-09-26T17:17:19+03:00" />
@ -46,7 +46,7 @@ I also fixed a few bugs and improved the region-matching logic
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<meta name="generator" content="Hugo 0.102.3" />
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@ -56,9 +56,9 @@ I also fixed a few bugs and improved the region-matching logic
"@type": "BlogPosting",
"headline": "September, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-09/",
"wordCount": "2677",
"wordCount": "3035",
"datePublished": "2022-09-01T09:41:36+03:00",
"dateModified": "2022-09-25T21:02:46+03:00",
"dateModified": "2022-09-26T17:17:19+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -622,7 +622,60 @@ X-Cache-Status: HIT
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
<h2 id="2022-09-27">2022-09-27</h2>
<ul>
<li>Find a few more ORCID identifiers missing for ILRI authors and add them to the controlled vocabulary and tag the authors on CGSpace</li>
<li>Moises from CIP says the WordPress importer worked fine with the current nginx proxy cache settings so it seems adding the HTTP Accept header to the cache key worked</li>
<li>Update my DSpace 7 environments to 7.4-SNAPSHOT
<ul>
<li>I see they have added thumbnails in some places now</li>
<li>Oh nice, they also added the &ldquo;recent submissions&rdquo; to the home page</li>
</ul>
</li>
<li>While talking with Salem about the MEL depositing to CGSpace we discovered an issue with HTTP DELETE on <code>/items/{item id}/bitstreams/{bitstream id}</code> or <code>/bitstreams/{bitstream id}</code>
<ul>
<li>DSpace removes the bitstream but keeps the empty <code>THUMBNAIL</code> bundle, which breaks the display in XMLUI</li>
</ul>
</li>
<li>Meeting with Enrico et al about PRMS reporting for the initiatives</li>
</ul>
<h2 id="2022-09-28">2022-09-28</h2>
<ul>
<li>I was reading the source code for DSpace 6&rsquo;s REST API and found that it&rsquo;s <a href="https://github.com/DSpace/DSpace/blob/dspace-6.4/dspace-rest/src/main/java/org/dspace/rest/ItemsResource.java#L427">not possible to specify a bundle while POSTing a bitstream</a>
<ul>
<li>I asked Salem how they do it on MEL and he said they pretend to be a human and do it via XMLUI!</li>
</ul>
</li>
<li>I added a few new ILRI subjects to the input forms on CGSpace
<ul>
<li>Both &ldquo;bushmeat&rdquo; and &ldquo;wildlife conservation&rdquo; are AGROVOC terms, but &ldquo;wild meat&rdquo; is not</li>
<li>The distinction ILRI would like to start making is:</li>
</ul>
</li>
</ul>
<blockquote>
<p>Meat comes from any animal, and when at ILRI we specifically make
reference to it in the context of livestock. However the word bushmeat
refers to illegal harvesting of meat. wild meat is being used as legal
harvesting of meat from wildlife and not from livestock.</p>
</blockquote>
<ul>
<li>I added a few more CGIAR authors ORCID identifiers to our controlled vocabulary and tagged them on CGSpace (~450 more metadata fields)</li>
<li>Talking to Salem about ORCID identifiers, we compared list and they have a bunch that we don&rsquo;t have:</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>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml ~/Downloads/MEL_ORCID_2022-09-28.csv | <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> grep -oE &#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39; | \
</span></span><span style="display:flex;"><span> sort | \
</span></span><span style="display:flex;"><span> uniq &gt; /tmp/2022-09-29-combined-orcids.txt
</span></span><span style="display:flex;"><span>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep -oE <span style="color:#e6db74">&#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39;</span> | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>1421
</span></span><span style="display:flex;"><span>$ wc -l /tmp/2022-09-29-combined-orcids.txt
</span></span><span style="display:flex;"><span>1905 /tmp/2022-09-29-combined-orcids.txt
</span></span></code></pre></div><ul>
<li>After combining them I ran them through my <code>resolve-orcids.py</code> script:</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>$ ./ilri/resolve-orcids.py -i /tmp/2022-09-29-combined-orcids.txt -o /tmp/2022-09-29-combined-orcids-names.txt -d
</span></span></code></pre></div><!-- raw HTML omitted -->