alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-17 20:27:05 +01:00
Code Issues Projects Releases Wiki Activity
74f4afe72a
cgspace-notes/docs/2023-07/index.html

351 lines
21 KiB
HTML
Raw Blame History

<!DOCTYPE html>
<html lang="en" >
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="July, 2023" />
<meta property="og:description" content="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 describe in my DSpace issue from last year: https://github." />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-07/" />
<meta property="article:published_time" content="2023-07-01T17:14:36+03:00" />
<meta property="article:modified_time" content="2023-07-19T12:27:43+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="July, 2023"/>
<meta name="twitter:description" content="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 describe in my DSpace issue from last year: https://github."/>
<meta name="generator" content="Hugo 0.112.3">
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "BlogPosting",
"headline": "July, 2023",
"url": "https://alanorth.github.io/cgspace-notes/2023-07/",
"wordCount": "1164",
"datePublished": "2023-07-01T17:14:36+03:00",
"dateModified": "2023-07-19T12:27:43+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
},
"keywords": "Notes"
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2023-07/">
<title>July, 2023 | CGSpace Notes</title>
<!-- combined, minified CSS -->
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F&#43;GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" crossorigin="anonymous">
<!-- minified Font Awesome for SVG icons -->
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz&#43;lcnA=" crossorigin="anonymous"></script>
<!-- RSS 2.0 feed -->
</head>
<body>
<div class="blog-masthead">
<div class="container">
<nav class="nav blog-nav">
<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
</nav>
</div>
</div>
<header class="blog-header">
<div class="container">
<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
</div>
</header>
<div class="container">
<div class="row">
<div class="col-sm-8 blog-main">
<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>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2023-07-01">2023-07-01</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start harvesting on AReS</li>
</ul>
<h2 id="2023-07-02">2023-07-02</h2>
<ul>
<li>Minor edits to the <code>crossref_doi_lookup.py</code> script while running some checks from 22,000 CGSpace DOIs</li>
</ul>
<h2 id="2023-07-03">2023-07-03</h2>
<ul>
<li>I analyzed the licenses declared by Crossref and found with high confidence that ~400 of ours were incorrect
<ul>
<li>I took the more accurate ones from Crossref and updated the items on CGSpace</li>
<li>I took a few hundred ISBNs as well for where we were missing them</li>
<li>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</li>
<li>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)</li>
<li>I would be curious to write a script to check the Unpaywall API for open access status&hellip;</li>
<li>In the past I found that their <em>license</em> status was not very accurate, but the open access status might be more reliable</li>
</ul>
</li>
<li>More minor work on the DSpace 7 item views
<ul>
<li>I learned some new Angular template syntax</li>
<li>I created a custom component to show Creative Commons licenses on the simple item page</li>
<li>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</li>
</ul>
</li>
</ul>
<h2 id="2023-07-04">2023-07-04</h2>
<ul>
<li>Focus group meeting with CGSpace partners about DSpace 7</li>
<li>I added a themed file selection component to the CGSpace theme
<ul>
<li>It displays the bistream description instead of the file name, just like we did in DSpace 6 XMLUI</li>
</ul>
</li>
<li>I added a custom component to show share icons</li>
</ul>
<h2 id="2023-07-05">2023-07-05</h2>
<ul>
<li>I spent some time trying to update OpenRXV from Angular 9 to 10 to 11 to 12 to 13
<ul>
<li>Most things work but there are some minor bugs it seems</li>
</ul>
</li>
<li>Mishell from CIP emailed me to say she was having problems approving an item on CGSpace
<ul>
<li>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</li>
</ul>
</li>
</ul>
<h2 id="2023-07-06">2023-07-06</h2>
<ul>
<li>Types meeting</li>
<li>I wrote a Python script to check Unpaywall for some information about DOIs</li>
</ul>
<h2 id="2023-07-7">2023-07-7</h2>
<ul>
<li>Continue exploring Unpaywall data for some of our DOIs
<ul>
<li>In the past I&rsquo;ve found their <em>licensing</em> information to not be very reliable (preferring Crossref), but I think their <em>open access status</em> is more reliable, especially when the provider is listed as being the publisher</li>
<li>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</li>
<li>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</li>
</ul>
</li>
<li>Delete duplicate metadata as describe in my DSpace issue from last year: <a href="https://github.com/DSpace/DSpace/issues/8253">https://github.com/DSpace/DSpace/issues/8253</a></li>
<li>Start working on some statistics on AGROVOC usage for my presenation next week
<ul>
<li>I used the following SQL query to dump values from all subject fields and lower case them:</li>
</ul>
</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>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS &#34;subject&#34; FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119)) to /tmp/2023-07-07-cgspace-subjects.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>COPY 26443
</span></span><span style="display:flex;"><span>Time: 2564.851 ms (00:02.565)
</span></span></code></pre></div><ul>
<li>Then I extracted the subjects and looked them up against AGROVOC:</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>$ csvcut -c subject /tmp/2023-07-07-cgspace-subjects.csv | sed <span style="color:#e6db74">&#39;1d&#39;</span> &gt; /tmp/2023-07-07-cgspace-subjects.txt
</span></span><span style="display:flex;"><span>$ ./ilri/agrovoc_lookup.py -i /tmp/2023-07-07-cgspace-subjects.txt -o /tmp/2023-07-07-cgspace-subjects-results.csv
</span></span></code></pre></div><ul>
<li>I did some more tests with Angular 13 on OpenRXV and found out why the repository type dropdown wasn&rsquo;t working
<ul>
<li>It was because of a missing 1-line JSON file in the data directory, which is runtime data, not code</li>
<li>I copied the data directory from the production serve and rebuild and the site is working well now</li>
<li>I did a full harvest with plugins and it worked!</li>
<li>So it seems Angular 13.4.0 will work, yay</li>
</ul>
</li>
</ul>
<h2 id="2023-07-08">2023-07-08</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings
<ul>
<li>Start a harvest on AReS</li>
</ul>
</li>
<li>The AGROVOC lookup finished, so I checked the number of matches:</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>$ csvgrep -c <span style="color:#e6db74">&#39;match type&#39;</span> -r <span style="color:#e6db74">&#39;^.+$&#39;</span> ~/Downloads/2023-07-07-cgspace-subjects-resolved.csv | sed 1d | wc -l
</span></span><span style="display:flex;"><span>12528
</span></span></code></pre></div><ul>
<li>So that&rsquo;s 12,528 out of 26,443 unique terms (47.3%)</li>
<li>I did a LOT of work on the OpenRXV frontend build dependencies to bring more in line with Angular 13</li>
</ul>
<h2 id="2023-07-10">2023-07-10</h2>
<ul>
<li>I did a lot more work on OpenRXV to test and update dependencies</li>
<li>I deployed the latest version on the production server</li>
</ul>
<h2 id="2023-07-12">2023-07-12</h2>
<ul>
<li>CGSpace upgrade meeting with Americas and Africa group</li>
</ul>
<h2 id="2023-07-13">2023-07-13</h2>
<ul>
<li>Michael Victor asked me to help Aditi extract some information from CGSpace
<ul>
<li>She was interested in journal articles published between 2018 and 2023 with a range of subjects related to drought, flooding, resilience, etc</li>
<li>I used an advanced query with some AGROVOC terms:</li>
</ul>
</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>dcterms.issued:[2018 TO 2023] AND dcterms.type:&#34;Journal Article&#34; AND (dcterms.subject:flooding OR dcterms.subject:flood OR dcterms.subject:&#34;extreme weather events&#34; OR dcterms.subject:drought OR dcterms.subject:&#34;drought resistance&#34; OR dcterms.subject:&#34;drought tolerance&#34; OR dcterms.subject:&#34;soil salinity&#34; OR dcterms.subject:&#34;pests of plants&#34; OR dcterms.subject:pests OR dcterms.subject:heat OR dcterms.subject:fertilizers OR dcterms.subject:&#34;fertilizer technology&#34; OR dcterms.subject:&#34;rice fields&#34; OR dcterms.subject:&#34;landscape conservation&#34; OR dcterms.subject:&#34;landscape restoration&#34; OR dcterms.subject:livestock)
</span></span></code></pre></div><ul>
<li>Interestingly, some variations of this same exact query produce no search results, and I see this error in the DSpace log:</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>org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse &#39;dcterms.issued:[2018 TO 2023] AND dcterms.type:&#34;Journal Article&#34; AND (dcterms.subject:flooding OR dcterms.subject:flood OR dcterms.subject:&#34;extreme weather events&#34; OR dcterms.subject:drought OR dcterms.subject:&#34;drought resistance&#34; OR dcterms.subject:&#34;drought tolerance&#34; OR dcterms.subject:&#34;soil salinity&#34; OR dcterms.subject:&#34;pests of plants&#34; OR dcterms.subject:pests OR dcterms.subject:heat OR dcterms.subject:fertilizers OR dcterms.subject:&#34;fertilizer technology&#34; OR dcterms.subject:&#34;rice fields&#34; OR dcterms.subject:livestock OR dcterms.subject:&#34;landscape conservation&#34; OR dcterms.subject:&#34;landscape restoration\&#34;\)&#39;: Lexical error at line 1, column 617. Encountered: &lt;EOF&gt; after : &#34;\&#34;landscape restoration\\\&#34;\\)&#34;
</span></span></code></pre></div><ul>
<li>It seems to be when there is a quoted search term at the end of the parenthesized group
<ul>
<li>For what it&rsquo;s worth this same query worked fine on DSpace 7.6</li>
</ul>
</li>
</ul>
<h2 id="2023-07-15">2023-07-15</h2>
<ul>
<li>Export CGSpace to fix missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-07-17">2023-07-17</h2>
<ul>
<li>Rasika had sent me a list of new ORCID identifiers for new IWMI staff so I combined them with our existing list and ran <code>resolve_orcids.py</code> to refresh the names in our database
<ul>
<li>I updated the list, updated names in the database, and tagged new authors with missing identifiers in existing items</li>
</ul>
</li>
</ul>
<h2 id="2023-07-18">2023-07-18</h2>
<ul>
<li>Meeting with IWMI, IRRI, and IITA colleagues about CGSpace upgrade plans</li>
<li>Maria from the Alliance mentioned having some submissions stuck on CGSpace
<ul>
<li>I looked and found a number of locks stuck for many nineteen, eighteen, and more hours&hellip;</li>
<li>I killed them and told her to try again</li>
</ul>
</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>$ psql &lt; locks-age.sql | less -S
</span></span><span style="display:flex;"><span>$ psql &lt; locks-age.sql | grep -E <span style="color:#e6db74">&#34; (19|18|17|16|12):&#34;</span> | awk -F<span style="color:#e6db74">&#34;|&#34;</span> <span style="color:#e6db74">&#39;{print $10}&#39;</span> | sort -u | xargs kill
</span></span></code></pre></div><h2 id="2023-07-19">2023-07-19</h2>
<ul>
<li>I had to kill a bunch more locked processes in PostgreSQL, I&rsquo;m not sure what&rsquo;s going on</li>
<li>After some discussion about an advanced search bug with Tim on Slack, I filed <a href="https://github.com/DSpace/DSpace/issues/8962">an issue on GitHub</a></li>
</ul>
<h2 id="2023-07-20">2023-07-20</h2>
<ul>
<li>I added a new metadata field for CGIAR Impact Platforms (<code>cg.subject.impactPlatform</code>) to CGSpace</li>
</ul>
<!-- raw HTML omitted -->
</article>
</div> <!-- /.blog-main -->
<aside class="col-sm-3 ml-auto blog-sidebar">
<section class="sidebar-module">
<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2023-07/">July, 2023</a></li>
<li><a href="/cgspace-notes/2023-06/">June, 2023</a></li>
<li><a href="/cgspace-notes/2023-05/">May, 2023</a></li>
<li><a href="/cgspace-notes/2023-04/">April, 2023</a></li>
<li><a href="/cgspace-notes/2023-03/">March, 2023</a></li>
</ol>
</section>
<section class="sidebar-module">
<h4>Links</h4>
<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>
</aside>
</div> <!-- /.row -->
</div> <!-- /.container -->
<footer class="blog-footer">
<p dir="auto">
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
</p>
<p>
<a href="#">Back to top</a>
</p>
</footer>
</body>
</html>
Reference in New Issue View Git Blame Copy Permalink