alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-29 01:48:19 +01:00
Code Issues Projects Releases Wiki Activity
79708bd30c
cgspace-notes/docs/2024-05/index.html
Alan Orth a5298945a3
Add notes for 2024-09
2024-09-09 10:20:09 +03:00

377 lines
19 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!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="May, 2024" />
<meta property="og:description" content="2024-05-01
I dumped all the CGSpace DOIs and resolved them with my crossref_doi_lookup.py script
Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-05/" />
<meta property="article:published_time" content="2024-05-01T10:39:00+03:00" />
<meta property="article:modified_time" content="2024-05-28T16:40:32+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2024"/>
<meta name="twitter:description" content="2024-05-01
I dumped all the CGSpace DOIs and resolved them with my crossref_doi_lookup.py script
Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc
"/>
<meta name="generator" content="Hugo 0.133.1">
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "BlogPosting",
"headline": "May, 2024",
"url": "https://alanorth.github.io/cgspace-notes/2024-05/",
"wordCount": "1076",
"datePublished": "2024-05-01T10:39:00+03:00",
"dateModified": "2024-05-28T16:40:32+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
},
"keywords": "Notes"
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2024-05/">
<title>May, 2024 | 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/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>
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>
<h2 id="2024-05-05">2024-05-05</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
</ul>
<h2 id="2024-05-06">2024-05-06</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
</ul>
<h2 id="2024-05-07">2024-05-07</h2>
<ul>
<li>Discuss RSS feeds and OpenSearch with IWMI
<ul>
<li>It seems our OpenSearch feed settings are using the defaults, so I need to copy some of those over from our old DSpace 6 branch</li>
</ul>
</li>
<li>I saw a patch for an interesting issue on DSpace GitHub: <a href="https://github.com/DSpace/DSpace/issues/9544">Error submitting or deleting items - URI too long when user is in a large number of groups</a>
<ul>
<li>I hadn&rsquo;t realized it, but we have lots of those errors:</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>$ zstdgrep -a <span style="color:#e6db74">&#39;URI Too Long&#39;</span> log/dspace.log-2024-04-* | wc -l
</span></span><span style="display:flex;"><span>1423
</span></span></code></pre></div><ul>
<li>Spend some time looking at duplicate DOIs again&hellip;</li>
</ul>
<h2 id="2024-05-08">2024-05-08</h2>
<ul>
<li>Spend some time looking at duplicate DOIs again&hellip;
<ul>
<li>I finally finished looking at the duplicate DOIs for journal articles</li>
<li>I updated the list of handle redirects and there are 386 of them!</li>
</ul>
</li>
</ul>
<h2 id="2024-05-09">2024-05-09</h2>
<ul>
<li>Spend some time working on the IFPRI 2020–2021 batch
<ul>
<li>I started by checking for exact duplicates (1.0 similarity) using DOI, type, and issue date</li>
</ul>
</li>
</ul>
<h2 id="2024-05-12">2024-05-12</h2>
<ul>
<li>I couldn&rsquo;t figure out how to do a complex join on withdrawn items along with their metadata, so I pull out a few like titles, handles, and provenance separately:</li>
</ul>
<pre tabindex="0"><code class="language-psql" data-lang="psql">dspace=# \COPY (SELECT i.uuid, m.text_value AS uri FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=25) TO /tmp/withdrawn-handles.csv CSV HEADER;
dspace=# \COPY (SELECT i.uuid, m.text_value AS title FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=64) TO /tmp/withdrawn-titles.csv CSV HEADER;
dspace=# \COPY (SELECT i.uuid, m.text_value AS submitted_by FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=28 AND m.text_value LIKE &#39;Submitted by%&#39;) TO /tmp/withdrawn-submitted-by.csv CSV HEADER;
</code></pre><ul>
<li>Then joined them:</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>$ csvjoin -c uuid /tmp/withdrawn-title.csv /tmp/withdrawn-handles.csv /tmp/withdrawn-submitted-by.csv &gt; /tmp/withdrawn.csv
</span></span></code></pre></div><ul>
<li>This gives me an insight into who submitted at 334 of the duplicates over the past few years&hellip;</li>
<li>I fixed a few hundred titles with leading/trailing whitespace, newlines, and ligatures like ff, fi, fl, ffi, and ffl</li>
</ul>
<h2 id="2024-05-13">2024-05-13</h2>
<ul>
<li>Export a list of IFPRI information products with handle links and CONTENTdm links:</li>
</ul>
<pre tabindex="0"><code>$ csvgrep -c &#39;dc.description.provenance[en_US]&#39; -m &#39;CONTENTdm&#39; cgspace.csv \
| csvcut -c &#39;id,dc.description.provenance[en_US],dc.identifier.uri[en_US]&#39; \
| tee /tmp/ifpri-redirects.csv \
| csvstat --count
2645
</code></pre><ul>
<li>I discovered the <code>/server/api/pid/find</code> endpoint today, which is much more direct and manageable than the <code>/server/api/discover/search/objects?query=</code> endpoint when trying to get metadata for a Handle (item, collection, or community)
<ul>
<li>The &ldquo;pid&rdquo; stands for permanent identifiers apparently, and we can use it like this:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>https://dspace7test.ilri.org/server/api/pid/find?id=10568/118424
</code></pre><h2 id="2024-05-15">2024-05-15</h2>
<ul>
<li>I got journal titles for 2,900 journal articles that were missing them from Crossref</li>
</ul>
<h2 id="2024-05-16">2024-05-16</h2>
<p>Helping IFPRI with some DSpace 7 API support, these are two queries for items issued in 2024:</p>
<ul>
<li><a href="https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued:2024">https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued:2024</a></li>
<li><a href="https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued_dt%3A%5B2024-01-01T00%3A00%3A00Z%20TO%20%2A%5D">https://dspace7test.ilri.org/server/api/discover/search/objects?query=dcterms.issued_dt%3A%5B2024-01-01T00%3A00%3A00Z%20TO%20%2A%5D</a> — note the Lucene search syntax is URL encoded version of <code>:[2024-01-01T00:00:00Z TO *]</code></li>
</ul>
<p>Both of them return the same number of results and seem identitical as far as I can see, but the second one uses Solr date indexes and requires the full Lucene datetime and range syntax</p>
<p>I wrote a new version of the <code>check_duplicates.py</code> script to help identify duplicates with different types</p>
<ul>
<li>Initially I called it <code>check_duplicates_fast.py</code> but it&rsquo;s actually not faster</li>
<li>I need to find a way to deal with duplicates from IFPRI&rsquo;s repository because there are some mismatched types&hellip;</li>
</ul>
<h2 id="2024-05-20">2024-05-20</h2>
<p>Continue working through alternative duplicate matching for IFPRI</p>
<ul>
<li>Their item types are sometimes different than ours&hellip;</li>
<li>One thing I think I can say for sure is that the default similarity factor in my script is 0.6, and I rarely see legitimate duplicates with such similarity so I might increase this to 0.7 to reduce the number of items I have to check</li>
<li>Also, the difference in issue dates is currently 365, but I should reduce that a bit, perhaps to 270 days (9 months)</li>
</ul>
<h2 id="2024-05-22">2024-05-22</h2>
<ul>
<li>Finalize and upload the IFPRI 2020–2021 batch set
<ul>
<li>I used a new technique to get missing licenses via Crossref (it&rsquo;s Python 2 because of OpenRefine&rsquo;s Jython):</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> urllib2
</span></span><span style="display:flex;"><span>
</span></span><span style="display:flex;"><span>doi <span style="color:#f92672">=</span> cells[<span style="color:#e6db74">&#39;cg.identifier.doi[en_US]&#39;</span>]<span style="color:#f92672">.</span>value
</span></span><span style="display:flex;"><span>url <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;https://api.crossref.org/works/&#34;</span> <span style="color:#f92672">+</span> doi
</span></span><span style="display:flex;"><span>useragent <span style="color:#f92672">=</span> <span style="color:#e6db74">&#34;Python (mailto:a.o@cgiar.org)&#34;</span>
</span></span><span style="display:flex;"><span>
</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">&#34;utf-8&#34;</span>), headers<span style="color:#f92672">=</span>{<span style="color:#e6db74">&#34;User-Agent&#34;</span> : useragent})
</span></span><span style="display:flex;"><span>get <span style="color:#f92672">=</span> urllib2<span style="color:#f92672">.</span>urlopen(request)
</span></span><span style="display:flex;"><span>
</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">&#39;utf-8&#39;</span>)
</span></span></code></pre></div><h2 id="2024-05-23">2024-05-23</h2>
<ul>
<li>Finalize last of the duplicates I found for the IFPRI 2020–2021 batch set (those that we missed initially due to mismatched types)</li>
<li>Export a new list of IFPRI redirects from CONTENTdm:</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;dc.description.provenance[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;Original URLs? from IFPRI CONTENTdm&#39;</span> cgspace.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c &#39;id,dc.description.provenance[en_US],dc.identifier.uri[en_US]&#39; \
</span></span><span style="display:flex;"><span> | tee /tmp/ifpri-redirects.csv \
</span></span><span style="display:flex;"><span> | csvstat --count
</span></span><span style="display:flex;"><span>4004
</span></span></code></pre></div><p>I found a way to get abstracts from PLOS</p>
<ul>
<li>They offer an API that returns XML including the JATS-formatted abstracts</li>
<li>I created a new column in OpenRefine by fetching specially crafted URLs based on the DOIs using this GREL:</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>&#34;https://journals.plos.org/plosone/article/file?id=&#34; + cells[&#39;doi&#39;].value + &#39;&amp;type=manuscript&#39;
</span></span></code></pre></div><p>Then used <code>value.parseXml()</code> on the resulting text to extract the abstract&rsquo;s text:</p>
<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>value.parseXml().select(&#34;abstract&#34;)[0].xmlText()
</span></span></code></pre></div><p>This doesn&rsquo;t preserve <code>&lt;p&gt;</code> tags though&hellip;</p>
<ul>
<li>Oh, nice, this does!</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>forEach(value.parseHtml().select(&#34;abstract p&#34;), i, i.htmlText()).join(&#34;\r\n\r\n&#34;)
</span></span></code></pre></div><p>For each paragraph inside an abstract, get the inner text and join them as one string separated by two newlines&hellip;</p>
<ul>
<li>Ah, some articles have multiple abstracts, for example: <a href="https://journals.plos.org/plosone/article/file?id=https://doi.org/10.1371/journal.pntd.0001859&amp;type=manuscript">https://journals.plos.org/plosone/article/file?id=https://doi.org/10.1371/journal.pntd.0001859&amp;type=manuscript</a></li>
<li>I need to select the abstract that does <strong>not</strong> have any attributes (using <a href="https://jsoup.org/apidocs/org/jsoup/select/Selector.html">Jsoup selector syntax</a>)</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>forEach(value.parseXml().select(&#34;abstract:not([*]) p&#34;), i, i.xmlText()).join(&#34;\r\n\r\n&#34;)
</span></span></code></pre></div><p>Testing <code>xsv</code> (Rust) versus <code>csvkit</code> (Python) to filter all items with DOIs from a DSpace dump with 118,000 items:</p>
<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>$ time xsv search -s doi <span style="color:#e6db74">&#39;doi\.org&#39;</span> /tmp/cgspace-minimal.csv | xsv <span style="color:#66d9ef">select</span> doi | xsv count
</span></span><span style="display:flex;"><span>27339
</span></span><span style="display:flex;"><span>xsv search -s doi &#39;doi\.org&#39; /tmp/cgspace-minimal.csv 0.06s user 0.03s system 98% cpu 0.091 total
</span></span><span style="display:flex;"><span>xsv select doi 0.02s user 0.02s system 40% cpu 0.091 total
</span></span><span style="display:flex;"><span>xsv count 0.01s user 0.00s system 9% cpu 0.090 total
</span></span><span style="display:flex;"><span>$ time csvgrep -c doi -m <span style="color:#e6db74">&#39;doi.org&#39;</span> /tmp/cgspace-minimal.csv | csvcut -c doi | csvstat --count
</span></span><span style="display:flex;"><span>27339
</span></span><span style="display:flex;"><span>csvgrep -c doi -m &#39;doi.org&#39; /tmp/cgspace-minimal.csv 1.15s user 0.06s system 95% cpu 1.273 total
</span></span><span style="display:flex;"><span>csvcut -c doi 0.42s user 0.05s system 36% cpu 1.283 total
</span></span><span style="display:flex;"><span>csvstat --count 0.20s user 0.03s system 18% cpu 1.298 total
</span></span></code></pre></div><h2 id="2024-05-27">2024-05-27</h2>
<ul>
<li>Working on IFPRI datasets batch migration
<ul>
<li>732 items total</li>
<li>6 duplicates on CGSpace</li>
<li>6 duplicates within set that need investigation</li>
</ul>
</li>
</ul>
<h2 id="2024-05-28">2024-05-28</h2>
<ul>
<li>I&rsquo;m thinking of increasing the frequency of thumbnail generation on CGSpace
<ul>
<li>Currently the <code>dspace filter-media</code> script runs once at 3AM for all media types and seems to take ~10 minutes to run for all 118,000 items&hellip;</li>
<li>I think I will make the thumbnailer run explicitly more often using <code>-p &quot;ImageMagick PDF Thumbnail&quot;</code></li>
</ul>
</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/2024-09/">September, 2024</a></li>
<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
<li><a href="/cgspace-notes/2024-05/">May, 2024</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