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Add notes for 2022-06-30

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Alan Orth 2022-06-30 16:48:03 +03:00
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content/posts/2022-06.md
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@ -246,13 +246,43 @@ for triple in agrovoc.search_triples(None, None, '"abalones"@en'):
## 2022-06-29 ## 2022-06-29
- Continue working on the list of non-AGROVOC subject to report to FAO - Continue working on the list of non-AGROVOC subject to report to FAO
- I got a one liner to get the list of non-AGROVOC subjects and join them with their counts: - I got a one liner to get the list of non-AGROVOC subjects and join them with their counts (updated to use regex in csvgrep):
```console ```console
$ csvgrep -c 'number of matches' -m 0 /tmp/2022-06-28-cgspace-subjects-results.csv \ $ csvgrep -c 'number of matches' -r '^0$' /tmp/2022-06-28-cgspace-subjects-results.csv \
| csvcut -c subject \ | csvcut -c subject \
| csvjoin -c subject /tmp/2022-06-28-cgspace-subjects.csv - \ | csvjoin -c subject /tmp/2022-06-28-cgspace-subjects.csv - \
> /tmp/2022-06-28-cgspace-non-agrovoc.csv > /tmp/2022-06-28-cgspace-non-agrovoc.csv
``` ```
## 2022-06-30
- Check some AfricaRice records for potential duplicates on CGSpace for Abenet:
```console
$ csvcut -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/Africarice_2ndBatch_ay.csv | sed '1s/line_number/id/' > /tmp/africarice.csv
$ csv-metadata-quality -i /tmp/africarice.csv -o /tmp/africarice-cleaned.csv -u
$ ./ilri/check-duplicates.py -i /tmp/africarice-cleaned.csv -u dspacetest -db dspacetest -p 'dom@in34sniper' -o /tmp/africarice-duplicates.csv
```
- Looking at the non-AGROVOC subjects again, I see some in our list that are duplicated in uppercase and lowercase, so I will run it again with all lowercase:
```console
localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS "subject", count(*) 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) GROUP BY "subject" ORDER BY count DESC) to /tmp/2022-06-30-cgspace-subjects.csv WITH CSV HEADER;
```
- Also, I see there might be something wrong with my csvjoin because nigeria shows up in the final list as having not matched...
- Ah, I was using `csvgrep -m 0` to find rows that didn't match, but that also matched items that had 10, 100, 50, etc...
- We need to use a regex:
```console
$ csvgrep -c 'number of matches' -r '^0$' /tmp/2022-06-30-cgspace-subjects-results.csv \
| csvcut -c subject \
| csvjoin -c subject /tmp/2022-06-30-cgspace-subjects.csv - \
> /tmp/2022-06-30-cgspace-non-agrovoc.csv
```
- Then I took all the terms with fifty or more occurences and put them on a Google Sheet
- There I started removing any term that was a variation of an existing AGROVOC term (like cowpea/cowpeas, policy/policies) or a compound concept
<!-- vim: set sw=2 ts=2: --> <!-- vim: set sw=2 ts=2: -->

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@ -26,7 +26,7 @@ There seem to be many more of these:
<meta property="og:type" content="article" /> <meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-06/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-06/" />
<meta property="article:published_time" content="2022-06-06T09:01:36+03:00" /> <meta property="article:published_time" content="2022-06-06T09:01:36+03:00" />
<meta property="article:modified_time" content="2022-06-26T18:11:33+03:00" /> <meta property="article:modified_time" content="2022-06-30T09:41:54+03:00" />
@ -58,9 +58,9 @@ There seem to be many more of these:
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "June, 2022", "headline": "June, 2022",
"url": "https://alanorth.github.io/cgspace-notes/2022-06/", "url": "https://alanorth.github.io/cgspace-notes/2022-06/",
"wordCount": "1520", "wordCount": "1761",
"datePublished": "2022-06-06T09:01:36+03:00", "datePublished": "2022-06-06T09:01:36+03:00",
"dateModified": "2022-06-26T18:11:33+03:00", "dateModified": "2022-06-30T09:41:54+03:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"
@ -394,15 +394,45 @@ There seem to be many more of these:
<ul> <ul>
<li>Continue working on the list of non-AGROVOC subject to report to FAO <li>Continue working on the list of non-AGROVOC subject to report to FAO
<ul> <ul>
<li>I got a one liner to get the list of non-AGROVOC subjects and join them with their counts:</li> <li>I got a one liner to get the list of non-AGROVOC subjects and join them with their counts (updated to use regex in csvgrep):</li>
</ul> </ul>
</li> </li>
</ul> </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;number of matches&#39;</span> -m <span style="color:#ae81ff">0</span> /tmp/2022-06-28-cgspace-subjects-results.csv <span style="color:#ae81ff">\ <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;number of matches&#39;</span> -r <span style="color:#e6db74">&#39;^0$&#39;</span> /tmp/2022-06-28-cgspace-subjects-results.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c subject \ </span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c subject \
</span></span><span style="display:flex;"><span> | csvjoin -c subject /tmp/2022-06-28-cgspace-subjects.csv - \ </span></span><span style="display:flex;"><span> | csvjoin -c subject /tmp/2022-06-28-cgspace-subjects.csv - \
</span></span><span style="display:flex;"><span> &gt; /tmp/2022-06-28-cgspace-non-agrovoc.csv </span></span><span style="display:flex;"><span> &gt; /tmp/2022-06-28-cgspace-non-agrovoc.csv
</span></span></code></pre></div><!-- raw HTML omitted --> </span></span></code></pre></div><h2 id="2022-06-30">2022-06-30</h2>
<ul>
<li>Check some AfricaRice records for potential duplicates on CGSpace for Abenet:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -l -c dc.title,dcterms.issued,dcterms.type ~/Downloads/Africarice_2ndBatch_ay.csv | sed <span style="color:#e6db74">&#39;1s/line_number/id/&#39;</span> &gt; /tmp/africarice.csv
</span></span><span style="display:flex;"><span>$ csv-metadata-quality -i /tmp/africarice.csv -o /tmp/africarice-cleaned.csv -u
</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/africarice-cleaned.csv -u dspacetest -db dspacetest -p <span style="color:#e6db74">&#39;dom@in34sniper&#39;</span> -o /tmp/africarice-duplicates.csv
</span></span></code></pre></div><ul>
<li>Looking at the non-AGROVOC subjects again, I see some in our list that are duplicated in uppercase and lowercase, so I will run it again with all lowercase:</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;, count(*) 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) GROUP BY &#34;subject&#34; ORDER BY count DESC) to /tmp/2022-06-30-cgspace-subjects.csv WITH CSV HEADER;
</span></span></code></pre></div><ul>
<li>Also, I see there might be something wrong with my csvjoin because nigeria shows up in the final list as having not matched&hellip;
<ul>
<li>Ah, I was using <code>csvgrep -m 0</code> to find rows that didn&rsquo;t match, but that also matched items that had 10, 100, 50, etc&hellip;</li>
<li>We need to use a regex:</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>$ csvgrep -c <span style="color:#e6db74">&#39;number of matches&#39;</span> -r <span style="color:#e6db74">&#39;^0$&#39;</span> /tmp/2022-06-30-cgspace-subjects-results.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvcut -c subject \
</span></span><span style="display:flex;"><span> | csvjoin -c subject /tmp/2022-06-30-cgspace-subjects.csv - \
</span></span><span style="display:flex;"><span> &gt; /tmp/2022-06-30-cgspace-non-agrovoc.csv
</span></span></code></pre></div><ul>
<li>Then I took all the terms with fifty or more occurences and put them on a Google Sheet
<ul>
<li>There I started removing any term that was a variation of an existing AGROVOC term (like cowpea/cowpeas, policy/policies) or a compound concept</li>
</ul>
</li>
</ul>
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:type" content="website" /> <meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2022-06-26T18:11:33+03:00" /> <meta property="og:updated_time" content="2022-06-30T09:41:54+03:00" />

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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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