Add notes for 2022-11-07

content/posts/2022-11.md

@@ -20,4 +20,102 @@ categories: ["Notes"]
 - Tim merged my [pull request to override the ImageMagick PDF density in DSpace 7](https://github.com/DSpace/DSpace/pull/8553)
   - I ported it to DSpace 6.x and submitted a pull request: https://github.com/DSpace/DSpace/pull/8560
 
+## 2022-11-02
+
+- I joined the FAO–CGIAR AGROVOC results sharing meeting
+  - From June to October, 2022 we suggested 39 new keywords, added 27 to AGROVOC, 4 rejected, and 9 still under discussion
+- Doing duplicate check on IFPRI's batch upload and I found one duplicate uploaded by IWMI earlier this year
+  - I will update the metadata of that item and map it to the correct Initiative collection
+
+## 2022-11-03
+
+- I added countries to the twenty-three IFPRI items in OpenRefine based on their titles and abstracts (using the Jython trick I learned a few months ago), then added regions using csv-metadata-quality, and uploaded them to CGSpace
+- I exported a list of collections from CGSpace so I can run the thumbnail fixes on each, as we seem to have issues when doing it on (some) large communities like the CRP community:
+
+```console
+localhost/dspace= ☘ \COPY (SELECT ds6_collection2collectionhandle(uuid) AS collection FROM collection) to /tmp/collections.txt
+COPY 1268
+```
+
+- Then I started a test run on DSpace Test:
+
+```console
+$ while read -r collection; do chrt -b 0 dspace dsrun io.github.ilri.cgspace.scripts.FixLowQualityThumbnails $collection | tee -a /tmp/FixLowQualityThumbnails.log; done < /tmp/collections.txt
+```
+
+- I'll be curious to check the log after it's all done.
+  - After a few hours I see:
+
+```console
+$ grep -c 'Action: remove' /tmp/FixLowQualityThumbnails.log 
+626
+```
+
+- Not bad, because last week I did a more manual selection of collections and deleted ~200
+  - I will replicate this on CGSpace soon, and also try the FixJpgJpgThumbnails tool
+- I see that the CIAT Library is still up, so I should really grab all the PDFs before they shut that old server down
+  - Export a list of items with PDFs linked there:
+
+```console
+localhost/dspacetest= ☘ \COPY (SELECT dspace_object_id,text_value FROM metadatavalue WHERE metadata_field_id=219 AND text_value LIKE '%ciat-library%') to /tmp/ciat-library-items.csv;
+COPY 4621
+```
+
+- After stripping the page numbers off I see there are only about 2,700 unique files, and we have to filter the dead JSPUI ones...
+
+```console
+$ csvcut -c url 2022-11-03-CIAT-Library-items.csv | sed 1d | grep -v jspui | sort -u | wc -l
+2752
+```
+
+- I'm not sure how we'll handle the duplicates because many items are book chapters or something where they share a PDF
+
+## 2022-11-04
+
+- I decided to check for old pre-ImageMagick thumbnails on CGSpace by finding any bitstreams with the description "Generated Thumbnail":
+
+```console
+localhost/dspacetest= ☘ \COPY (SELECT ds6_bitstream2itemhandle(dspace_object_id) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND text_value='Generated Thumbnail') to /tmp/old-thumbnails.txt;
+COPY 1147
+$ grep -v '\\N' /tmp/old-thumbnails.txt > /tmp/old-thumbnail-handles.txt
+$ wc -l /tmp/old-thumbnail-handles.txt 
+987 /tmp/old-thumbnail-handles.txt
+```
+
+- A bunch of these have `\N` for some reason when I use the `ds6_bitstream2itemhandle` function to get their handles so I had to exclude those...
+  - I forced the media-filter for these items on CGSpace:
+
+```console
+$ while read -r handle; do JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" dspace filter-media -p "ImageMagick PDF Thumbnail" -i $handle -f -v; done < /tmp/old-thumbnail-handles.txt
+```
+
+- Upload some batch records via CSV for Peter
+- Update the about page on CGSpace with new text from Peter
+- Add a few more ORCID identifiers and names to my growing file `2022-09-22-add-orcids.csv`
+  - I tagged fifty-four new authors using this list
+- I deleted and mapped one duplicate item for Maria Garruccio
+- I updated the CG Core website from Bootstrap v4.6 to v5.2
+
+## 2022-11-07
+
+- I did a harvest on AReS last night but it seems that MELSpace's sitemap is broken again because we have 10,000 fewer records
+- I filed [an issue](https://github.com/ecrmnn/iso-3166-1/issues/10) on the iso-3166-1 npm package to update the name of Turkey to Türkiye
+  - I also filed [an issue](https://github.com/flyingcircusio/pycountry/issues/148) and [a pull request](https://github.com/flyingcircusio/pycountry/pull/149) on the pycountry package
+  - I also filed [an issue](https://github.com/konstantinstadler/country_converter/issues/121) and [a pull request](https://github.com/konstantinstadler/country_converter/pull/122) on the country-converter package
+  - I also changed one item on CGSpace that had been submitted since the name was changed
+  - I also imported the new iso-codes 4.12.0 into cgspace-java-helpers
+  - I also updated it in the DSpace `input-forms.xml`
+  - I also forked the iso-3166-1 package from npm and updated Swaziland, Macedonia, and Turkey in my fork
+    - I submitted a [pull request](https://github.com/ecrmnn/iso-3166-1/pull/11) to update this upstream
+- Since I was making all these pull requests I also made [one on country-converter for the UN M.49 region "South-eastern Asia"](https://github.com/konstantinstadler/country_converter/pull/123)
+- Port the [ImageMagick PDF cropbox fix](https://github.com/DSpace/DSpace/pull/8550) to DSpace 6.x
+  - I deployed it on CGSpace, ran all updates, and rebooted the host
+  - I ran the filter-media script on one large collection where many of these PDFs with cropbox issues exist:
+
+```console
+$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace filter-media -p "ImageMagick PDF Thumbnail" -v -f -i 10568/78 >& /tmp/filter-media-cropbox.log
+```
+
+- But looking at the items it processed, I'm not sure it's working as expected
+
 <!-- vim: set sw=2 ts=2: -->

docs/2022-11/index.html

@@ -24,7 +24,7 @@ I reverted the Cocoon autosave change because it was more of a nuissance that Pe
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-11/" />
 <meta property="article:published_time" content="2022-11-01T09:11:36+03:00" />
-<meta property="article:modified_time" content="2022-11-01T09:11:36+03:00" />
+<meta property="article:modified_time" content="2022-11-01T22:12:24+03:00" />
 
 
 
@@ -54,9 +54,9 @@ I reverted the Cocoon autosave change because it was more of a nuissance that Pe
   "@type": "BlogPosting",
   "headline": "November, 2022",
   "url": "https://alanorth.github.io/cgspace-notes/2022-11/",
-  "wordCount": "134",
+  "wordCount": "863",
   "datePublished": "2022-11-01T09:11:36+03:00",
-  "dateModified": "2022-11-01T09:11:36+03:00",
+  "dateModified": "2022-11-01T22:12:24+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -153,6 +153,118 @@ I reverted the Cocoon autosave change because it was more of a nuissance that Pe
 </ul>
 </li>
 </ul>
+<h2 id="2022-11-02">2022-11-02</h2>
+<ul>
+<li>I joined the FAO–CGIAR AGROVOC results sharing meeting
+<ul>
+<li>From June to October, 2022 we suggested 39 new keywords, added 27 to AGROVOC, 4 rejected, and 9 still under discussion</li>
+</ul>
+</li>
+<li>Doing duplicate check on IFPRI&rsquo;s batch upload and I found one duplicate uploaded by IWMI earlier this year
+<ul>
+<li>I will update the metadata of that item and map it to the correct Initiative collection</li>
+</ul>
+</li>
+</ul>
+<h2 id="2022-11-03">2022-11-03</h2>
+<ul>
+<li>I added countries to the twenty-three IFPRI items in OpenRefine based on their titles and abstracts (using the Jython trick I learned a few months ago), then added regions using csv-metadata-quality, and uploaded them to CGSpace</li>
+<li>I exported a list of collections from CGSpace so I can run the thumbnail fixes on each, as we seem to have issues when doing it on (some) large communities like the CRP community:</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/dspace= ☘ \COPY (SELECT ds6_collection2collectionhandle(uuid) AS collection FROM collection) to /tmp/collections.txt
+</span></span><span style="display:flex;"><span>COPY 1268
+</span></span></code></pre></div><ul>
+<li>Then I started a test run on DSpace Test:</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>$ <span style="color:#66d9ef">while</span> read -r collection; <span style="color:#66d9ef">do</span> chrt -b <span style="color:#ae81ff">0</span> dspace dsrun io.github.ilri.cgspace.scripts.FixLowQualityThumbnails $collection | tee -a /tmp/FixLowQualityThumbnails.log; <span style="color:#66d9ef">done</span> &lt; /tmp/collections.txt
+</span></span></code></pre></div><ul>
+<li>I&rsquo;ll be curious to check the log after it&rsquo;s all done.
+<ul>
+<li>After a few hours I see:</li>
+</ul>
+</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ grep -c <span style="color:#e6db74">&#39;Action: remove&#39;</span> /tmp/FixLowQualityThumbnails.log 
+</span></span><span style="display:flex;"><span>626
+</span></span></code></pre></div><ul>
+<li>Not bad, because last week I did a more manual selection of collections and deleted ~200
+<ul>
+<li>I will replicate this on CGSpace soon, and also try the FixJpgJpgThumbnails tool</li>
+</ul>
+</li>
+<li>I see that the CIAT Library is still up, so I should really grab all the PDFs before they shut that old server down
+<ul>
+<li>Export a list of items with PDFs linked there:</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 dspace_object_id,text_value FROM metadatavalue WHERE metadata_field_id=219 AND text_value LIKE &#39;%ciat-library%&#39;) to /tmp/ciat-library-items.csv;
+</span></span><span style="display:flex;"><span>COPY 4621
+</span></span></code></pre></div><ul>
+<li>After stripping the page numbers off I see there are only about 2,700 unique files, and we have to filter the dead JSPUI ones&hellip;</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 url 2022-11-03-CIAT-Library-items.csv | sed 1d | grep -v jspui | sort -u | wc -l
+</span></span><span style="display:flex;"><span>2752
+</span></span></code></pre></div><ul>
+<li>I&rsquo;m not sure how we&rsquo;ll handle the duplicates because many items are book chapters or something where they share a PDF</li>
+</ul>
+<h2 id="2022-11-04">2022-11-04</h2>
+<ul>
+<li>I decided to check for old pre-ImageMagick thumbnails on CGSpace by finding any bitstreams with the description &ldquo;Generated Thumbnail&rdquo;:</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 ds6_bitstream2itemhandle(dspace_object_id) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND text_value=&#39;Generated Thumbnail&#39;) to /tmp/old-thumbnails.txt;
+</span></span><span style="display:flex;"><span>COPY 1147
+</span></span><span style="display:flex;"><span>$ grep -v <span style="color:#e6db74">&#39;\\N&#39;</span> /tmp/old-thumbnails.txt &gt; /tmp/old-thumbnail-handles.txt
+</span></span><span style="display:flex;"><span>$ wc -l /tmp/old-thumbnail-handles.txt 
+</span></span><span style="display:flex;"><span>987 /tmp/old-thumbnail-handles.txt
+</span></span></code></pre></div><ul>
+<li>A bunch of these have <code>\N</code> for some reason when I use the <code>ds6_bitstream2itemhandle</code> function to get their handles so I had to exclude those&hellip;
+<ul>
+<li>I forced the media-filter for these items on CGSpace:</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>$ <span style="color:#66d9ef">while</span> read -r handle; <span style="color:#66d9ef">do</span> JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx512m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</span> -i $handle -f -v; <span style="color:#66d9ef">done</span> &lt; /tmp/old-thumbnail-handles.txt
+</span></span></code></pre></div><ul>
+<li>Upload some batch records via CSV for Peter</li>
+<li>Update the about page on CGSpace with new text from Peter</li>
+<li>Add a few more ORCID identifiers and names to my growing file <code>2022-09-22-add-orcids.csv</code>
+<ul>
+<li>I tagged fifty-four new authors using this list</li>
+</ul>
+</li>
+<li>I deleted and mapped one duplicate item for Maria Garruccio</li>
+<li>I updated the CG Core website from Bootstrap v4.6 to v5.2</li>
+</ul>
+<h2 id="2022-11-07">2022-11-07</h2>
+<ul>
+<li>I did a harvest on AReS last night but it seems that MELSpace&rsquo;s sitemap is broken again because we have 10,000 fewer records</li>
+<li>I filed <a href="https://github.com/ecrmnn/iso-3166-1/issues/10">an issue</a> on the iso-3166-1 npm package to update the name of Turkey to Türkiye
+<ul>
+<li>I also filed <a href="https://github.com/flyingcircusio/pycountry/issues/148">an issue</a> and <a href="https://github.com/flyingcircusio/pycountry/pull/149">a pull request</a> on the pycountry package</li>
+<li>I also filed <a href="https://github.com/konstantinstadler/country_converter/issues/121">an issue</a> and <a href="https://github.com/konstantinstadler/country_converter/pull/122">a pull request</a> on the country-converter package</li>
+<li>I also changed one item on CGSpace that had been submitted since the name was changed</li>
+<li>I also imported the new iso-codes 4.12.0 into cgspace-java-helpers</li>
+<li>I also updated it in the DSpace <code>input-forms.xml</code></li>
+<li>I also forked the iso-3166-1 package from npm and updated Swaziland, Macedonia, and Turkey in my fork
+<ul>
+<li>I submitted a <a href="https://github.com/ecrmnn/iso-3166-1/pull/11">pull request</a> to update this upstream</li>
+</ul>
+</li>
+</ul>
+</li>
+<li>Since I was making all these pull requests I also made <a href="https://github.com/konstantinstadler/country_converter/pull/123">one on country-converter for the UN M.49 region &ldquo;South-eastern Asia&rdquo;</a></li>
+<li>Port the <a href="https://github.com/DSpace/DSpace/pull/8550">ImageMagick PDF cropbox fix</a> to DSpace 6.x
+<ul>
+<li>I deployed it on CGSpace, ran all updates, and rebooted the host</li>
+<li>I ran the filter-media script on one large collection where many of these PDFs with cropbox issues exist:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</span> -v -f -i 10568/78 &gt;&amp; /tmp/filter-media-cropbox.log
+</span></span></code></pre></div><ul>
+<li>But looking at the items it processed, I&rsquo;m not sure it&rsquo;s working as expected</li>
+</ul>
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docs/page/7/index.html

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docs/page/8/index.html

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docs/page/9/index.html

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