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Add notes for 2024-05-27
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@ -106,4 +106,86 @@ Continue working through alternative duplicate matching for IFPRI
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- 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
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- Also, the difference in issue dates is currently 365, but I should reduce that a bit, perhaps to 270 days (9 months)
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## 2024-05-22
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- Finalize and upload the IFPRI 2020–2021 batch set
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- I used a new technique to get missing licenses via Crossref (it's Python 2 because of OpenRefine's Jython):
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```python
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import urllib2
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doi = cells['cg.identifier.doi[en_US]'].value
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url = "https://api.crossref.org/works/" + doi
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useragent = "Python (mailto:a.o@cgiar.org)"
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request = urllib2.Request(url.encode("utf-8"), headers={"User-Agent" : useragent})
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get = urllib2.urlopen(request)
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return get.read().decode('utf-8')
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```
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## 2024-05-23
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- Finalize last of the duplicates I found for the IFPRI 2020–2021 batch set (those that we missed initially due to mismatched types)
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- Export a new list of IFPRI redirects from CONTENTdm:
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```console
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$ csvgrep -c 'dc.description.provenance[en_US]' -r 'Original URLs? from IFPRI CONTENTdm' cgspace.csv \
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| csvcut -c 'id,dc.description.provenance[en_US],dc.identifier.uri[en_US]' \
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| tee /tmp/ifpri-redirects.csv \
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| csvstat --count
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4004
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```
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I found a way to get abstracts from PLOS
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- They offer an API that returns XML including the JATS-formatted abstracts
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- I created a new column in OpenRefine by fetching specially crafted URLs based on the DOIs using this GREL:
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```console
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"https://journals.plos.org/plosone/article/file?id=" + cells['doi'].value + '&type=manuscript'
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```
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Then used `value.parseXml()` on the resulting text to extract the abstract's text:
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```console
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value.parseXml().select("abstract")[0].xmlText()
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```
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This doesn't preserve `<p>` tags though...
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- Oh, nice, this does!
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```console
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forEach(value.parseHtml().select("abstract p"), i, i.htmlText()).join("\r\n\r\n")
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```
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For each paragraph inside an abstract, get the inner text and join them as one string separated by two newlines...
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- 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
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- 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))
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```console
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forEach(value.parseXml().select("abstract:not([*]) p"), i, i.xmlText()).join("\r\n\r\n")
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```
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Testing `xsv` (Rust) versus `csvkit` (Python) to filter all items with DOIs from a DSpace dump with 118,000 items:
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```console
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$ time xsv search -s doi 'doi\.org' /tmp/cgspace-minimal.csv | xsv select doi | xsv count
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27339
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xsv search -s doi 'doi\.org' /tmp/cgspace-minimal.csv 0.06s user 0.03s system 98% cpu 0.091 total
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xsv select doi 0.02s user 0.02s system 40% cpu 0.091 total
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xsv count 0.01s user 0.00s system 9% cpu 0.090 total
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$ time csvgrep -c doi -m 'doi.org' /tmp/cgspace-minimal.csv | csvcut -c doi | csvstat --count
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27339
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csvgrep -c doi -m 'doi.org' /tmp/cgspace-minimal.csv 1.15s user 0.06s system 95% cpu 1.273 total
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csvcut -c doi 0.42s user 0.05s system 36% cpu 1.283 total
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csvstat --count 0.20s user 0.03s system 18% cpu 1.298 total
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```
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## 2024-05-27
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- Working on IFPRI datasets batch migration
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- 732 items total
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- 6 duplicates on CGSpace
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- 6 duplicates within set that need investigation
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<!-- vim: set sw=2 ts=2: -->
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@ -18,7 +18,7 @@ Then I did some work to add missing abstracts (about 900!), volumes, issues, lic
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-05/" />
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<meta property="article:published_time" content="2024-05-01T10:39:00+03:00" />
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<meta property="article:modified_time" content="2024-05-13T16:24:11+03:00" />
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<meta property="article:modified_time" content="2024-05-20T17:34:14+03:00" />
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@ -42,9 +42,9 @@ Then I did some work to add missing abstracts (about 900!), volumes, issues, lic
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"@type": "BlogPosting",
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"headline": "May, 2024",
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"url": "https://alanorth.github.io/cgspace-notes/2024-05/",
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"wordCount": "652",
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"wordCount": "1023",
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"datePublished": "2024-05-01T10:39:00+03:00",
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"dateModified": "2024-05-13T16:24:11+03:00",
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"dateModified": "2024-05-20T17:34:14+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -224,6 +224,74 @@ dspace=# \COPY (SELECT i.uuid, m.text_value AS submitted_by FROM item i JOIN met
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<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>
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<li>Also, the difference in issue dates is currently 365, but I should reduce that a bit, perhaps to 270 days (9 months)</li>
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</ul>
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<h2 id="2024-05-22">2024-05-22</h2>
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<ul>
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<li>Finalize and upload the IFPRI 2020–2021 batch set
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<ul>
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<li>I used a new technique to get missing licenses via Crossref (it’s Python 2 because of OpenRefine’s Jython):</li>
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</ul>
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</li>
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</ul>
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<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
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</span></span><span style="display:flex;"><span>
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</span></span><span style="display:flex;"><span>doi <span style="color:#f92672">=</span> cells[<span style="color:#e6db74">'cg.identifier.doi[en_US]'</span>]<span style="color:#f92672">.</span>value
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</span></span><span style="display:flex;"><span>url <span style="color:#f92672">=</span> <span style="color:#e6db74">"https://api.crossref.org/works/"</span> <span style="color:#f92672">+</span> doi
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</span></span><span style="display:flex;"><span>useragent <span style="color:#f92672">=</span> <span style="color:#e6db74">"Python (mailto:a.o@cgiar.org)"</span>
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</span></span><span style="display:flex;"><span>
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</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">"utf-8"</span>), headers<span style="color:#f92672">=</span>{<span style="color:#e6db74">"User-Agent"</span> : useragent})
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</span></span><span style="display:flex;"><span>get <span style="color:#f92672">=</span> urllib2<span style="color:#f92672">.</span>urlopen(request)
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</span></span><span style="display:flex;"><span>
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</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">'utf-8'</span>)
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</span></span></code></pre></div><h2 id="2024-05-23">2024-05-23</h2>
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<ul>
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<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>
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<li>Export a new list of IFPRI redirects from CONTENTdm:</li>
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</ul>
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<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">'dc.description.provenance[en_US]'</span> -r <span style="color:#e6db74">'Original URLs? from IFPRI CONTENTdm'</span> cgspace.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c 'id,dc.description.provenance[en_US],dc.identifier.uri[en_US]' \
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</span></span><span style="display:flex;"><span> | tee /tmp/ifpri-redirects.csv \
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</span></span><span style="display:flex;"><span> | csvstat --count
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</span></span><span style="display:flex;"><span>4004
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</span></span></code></pre></div><p>I found a way to get abstracts from PLOS</p>
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<ul>
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<li>They offer an API that returns XML including the JATS-formatted abstracts</li>
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<li>I created a new column in OpenRefine by fetching specially crafted URLs based on the DOIs using this GREL:</li>
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</ul>
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<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>"https://journals.plos.org/plosone/article/file?id=" + cells['doi'].value + '&type=manuscript'
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</span></span></code></pre></div><p>Then used <code>value.parseXml()</code> on the resulting text to extract the abstract’s text:</p>
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<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("abstract")[0].xmlText()
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</span></span></code></pre></div><p>This doesn’t preserve <code><p></code> tags though…</p>
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<ul>
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<li>Oh, nice, this does!</li>
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</ul>
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<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("abstract p"), i, i.htmlText()).join("\r\n\r\n")
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</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…</p>
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<ul>
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<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&type=manuscript">https://journals.plos.org/plosone/article/file?id=https://doi.org/10.1371/journal.pntd.0001859&type=manuscript</a></li>
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<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>
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</ul>
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<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("abstract:not([*]) p"), i, i.xmlText()).join("\r\n\r\n")
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</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>
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<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">'doi\.org'</span> /tmp/cgspace-minimal.csv | xsv <span style="color:#66d9ef">select</span> doi | xsv count
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</span></span><span style="display:flex;"><span>27339
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</span></span><span style="display:flex;"><span>xsv search -s doi 'doi\.org' /tmp/cgspace-minimal.csv 0.06s user 0.03s system 98% cpu 0.091 total
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</span></span><span style="display:flex;"><span>xsv select doi 0.02s user 0.02s system 40% cpu 0.091 total
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</span></span><span style="display:flex;"><span>xsv count 0.01s user 0.00s system 9% cpu 0.090 total
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</span></span><span style="display:flex;"><span>$ time csvgrep -c doi -m <span style="color:#e6db74">'doi.org'</span> /tmp/cgspace-minimal.csv | csvcut -c doi | csvstat --count
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</span></span><span style="display:flex;"><span>27339
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</span></span><span style="display:flex;"><span>csvgrep -c doi -m 'doi.org' /tmp/cgspace-minimal.csv 1.15s user 0.06s system 95% cpu 1.273 total
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</span></span><span style="display:flex;"><span>csvcut -c doi 0.42s user 0.05s system 36% cpu 1.283 total
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</span></span><span style="display:flex;"><span>csvstat --count 0.20s user 0.03s system 18% cpu 1.298 total
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</span></span></code></pre></div><h2 id="2024-05-27">2024-05-27</h2>
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<ul>
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<li>Working on IFPRI datasets batch migration
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<ul>
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<li>732 items total</li>
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<li>6 duplicates on CGSpace</li>
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<li>6 duplicates within set that need investigation</li>
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</ul>
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</li>
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</ul>
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<!-- raw HTML omitted -->
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@ -10,7 +10,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:updated_time" content="2024-05-20T17:34:14+03:00" />
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@ -6,7 +6,7 @@
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<description>Recent content in Categories on CGSpace Notes</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<lastBuildDate>Thu, 16 May 2024 08:27:56 +0300</lastBuildDate>
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<lastBuildDate>Mon, 20 May 2024 17:34:14 +0300</lastBuildDate>
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<atom:link href="https://alanorth.github.io/cgspace-notes/categories/index.xml" rel="self" type="application/rss+xml" />
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<item>
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<title>Notes</title>
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:updated_time" content="2024-05-20T17:34:14+03:00" />
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@ -6,7 +6,7 @@
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<description>Recent content in Notes on CGSpace Notes</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<lastBuildDate>Thu, 16 May 2024 08:27:56 +0300</lastBuildDate>
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<lastBuildDate>Mon, 20 May 2024 17:34:14 +0300</lastBuildDate>
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<atom:link href="https://alanorth.github.io/cgspace-notes/categories/notes/index.xml" rel="self" type="application/rss+xml" />
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<item>
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<title>May, 2024</title>
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:updated_time" content="2024-05-20T17:34:14+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:updated_time" content="2024-05-20T17:34:14+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:updated_time" content="2024-05-16T08:27:56+03:00" />
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|
Loading…
Reference in New Issue
Block a user