Add notes for 2024-05-27

2024-09-07 19:08:26 +02:00 · 2024-05-27 21:40:09 +03:00 · 2024-05-27 21:40:09 +03:00 · befe3a3a58
commit befe3a3a58
parent 39d8d0876c
39 changed files with 194 additions and 44 deletions
--- a/content/posts/2024-05.md
+++ b/content/posts/2024-05.md
@ -106,4 +106,86 @@ Continue working through alternative duplicate matching for IFPRI
  - 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
  - Also, the difference in issue dates is currently 365, but I should reduce that a bit, perhaps to 270 days (9 months)

+## 2024-05-22
+
+- Finalize and upload the IFPRI 2020–2021 batch set
+  - I used a new technique to get missing licenses via Crossref (it's Python 2 because of OpenRefine's Jython):
+
+```python
+import urllib2
+
+doi = cells['cg.identifier.doi[en_US]'].value
+url = "https://api.crossref.org/works/" + doi
+useragent = "Python (mailto:a.o@cgiar.org)"
+
+request = urllib2.Request(url.encode("utf-8"), headers={"User-Agent" : useragent})
+get = urllib2.urlopen(request)
+
+return get.read().decode('utf-8')
+```
+
+## 2024-05-23
+
+- Finalize last of the duplicates I found for the IFPRI 2020–2021 batch set (those that we missed initially due to mismatched types)
+- Export a new list of IFPRI redirects from CONTENTdm:
+
+```console
+$ csvgrep -c 'dc.description.provenance[en_US]' -r 'Original URLs? from IFPRI CONTENTdm' cgspace.csv \
+  | csvcut -c 'id,dc.description.provenance[en_US],dc.identifier.uri[en_US]' \
+  | tee /tmp/ifpri-redirects.csv \
+  | csvstat --count
+4004
+```
+
+I found a way to get abstracts from PLOS
+  - They offer an API that returns XML including the JATS-formatted abstracts
+  - I created a new column in OpenRefine by fetching specially crafted URLs based on the DOIs using this GREL:
+
+```console
+"https://journals.plos.org/plosone/article/file?id=" + cells['doi'].value + '&type=manuscript'
+```
+
+Then used `value.parseXml()` on the resulting text to extract the abstract's text:
+
+```console
+value.parseXml().select("abstract")[0].xmlText()
+```
+
+This doesn't preserve `<p>` tags though...
+  - Oh, nice, this does!
+
+```console
+forEach(value.parseHtml().select("abstract p"), i, i.htmlText()).join("\r\n\r\n")
+```
+
+For each paragraph inside an abstract, get the inner text and join them as one string separated by two newlines...
+  - Ah, some articles have multiple abstracts, for example: https://journals.plos.org/plosone/article/file?id=https://doi.org/10.1371/journal.pntd.0001859&type=manuscript
+  - I need to select the abstract that does **not** have any attributes (using [Jsoup selector syntax](https://jsoup.org/apidocs/org/jsoup/select/Selector.html))
+
+```console
+forEach(value.parseXml().select("abstract:not([*]) p"), i, i.xmlText()).join("\r\n\r\n")
+```
+
+Testing `xsv` (Rust) versus `csvkit` (Python) to filter all items with DOIs from a DSpace dump with 118,000 items:
+
+```console
+$ time xsv search -s doi 'doi\.org' /tmp/cgspace-minimal.csv | xsv select doi | xsv count
+27339
+xsv search -s doi 'doi\.org' /tmp/cgspace-minimal.csv  0.06s user 0.03s system 98% cpu 0.091 total
+xsv select doi  0.02s user 0.02s system 40% cpu 0.091 total
+xsv count  0.01s user 0.00s system 9% cpu 0.090 total
+$ time csvgrep -c doi -m 'doi.org' /tmp/cgspace-minimal.csv | csvcut -c doi | csvstat --count
+27339
+csvgrep -c doi -m 'doi.org' /tmp/cgspace-minimal.csv  1.15s user 0.06s system 95% cpu 1.273 total
+csvcut -c doi  0.42s user 0.05s system 36% cpu 1.283 total
+csvstat --count  0.20s user 0.03s system 18% cpu 1.298 total
+```
+
+## 2024-05-27
+
+- Working on IFPRI datasets batch migration
+  - 732 items total
+  - 6 duplicates on CGSpace
+  - 6 duplicates within set that need investigation
+
 <!-- vim: set sw=2 ts=2: -->
--- a/docs/2024-05/index.html
+++ b/docs/2024-05/index.html
@ -18,7 +18,7 @@ Then I did some work to add missing abstracts (about 900!), volumes, issues, lic
 <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="2024-05-13T16:24:11+03:00" />
+<meta property="article:modified_time" content="2024-05-20T17:34:14+03:00" />



@ -42,9 +42,9 @@ Then I did some work to add missing abstracts (about 900!), volumes, issues, lic
  "@type": "BlogPosting",
  "headline": "May, 2024",
  "url": "https://alanorth.github.io/cgspace-notes/2024-05/",
-  "wordCount": "652",
+  "wordCount": "1023",
  "datePublished": "2024-05-01T10:39:00+03:00",
-  "dateModified": "2024-05-13T16:24:11+03:00",
+  "dateModified": "2024-05-20T17:34:14+03:00",
  "author": {
    "@type": "Person",
    "name": "Alan Orth"
@ -224,6 +224,74 @@ dspace=# \COPY (SELECT i.uuid, m.text_value AS submitted_by FROM item i JOIN met
 <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>
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