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Add notes for 2023-04-20

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Alan Orth 2023-04-20 22:44:18 -07:00
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content/posts/2023-04.md
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@ -438,9 +438,11 @@ $ psql < locks-age.sql | grep -E "[[:digit:]] days" | awk -F\| '{print $10}' | s
- I ended up with a long list of UUIDs to fix before the script would complete:
```console
$ psql -d dspace -c "update bundle set primary_bitstream_id=NULL where primary_bitstream_id in ('a7ddf477-1c04-4de0-9c7a-4d3c84a875bc', '9582b661-9c2d-4c86-be22-c3b0942b646a', '210a4d5d-3af9-46f0-84cc-682dd1431762')"
$ psql -d dspace -c "update bundle set primary_bitstream_id=NULL where primary_bitstream_id in ('a7ddf477-1c04-4de0-9c7a-4d3c84a875bc', '9582b661-9c2d-4c86-be22-c3b0942b646a', '210a4d5d-3af9-46f0-84cc-682dd1431762', '51115f07-0a60-4988-8536-b9ebd2a5e15e', '0fc5021d-3264-413a-b2e2-74bda38a394e', '4704fa62-b8ab-4dfe-b7aa-0e4905f8412a')"
```
- This process ended up taking a few days because each iteration ran for over four hours before failing on the next UUID, sighhhhh
## 2023-04-18
- Regarding the item Abenet noticed yesterday that has a blank page and a nullPointerException
@ -448,4 +450,37 @@ $ psql -d dspace -c "update bundle set primary_bitstream_id=NULL where primary_b
- And according to the REST API on CGSpace the item was modified on 2023-04-11, so last week...
- According to the DSpace logs it was Francesca who edited the item last week, so I asked her for more information before I troubleshoot more
## 2023-04-19
- I fixed the Bioversity item by deleting the `9781138781276.jpg` bitstream via the REST API
- I *think* Francesca might have changed the "format" of it?
- Anyway, this item has a PDF so we have a proper thumbnail and don't need that other journal cover one
- I noticed a URL for this [Bioversity item](https://hdl.handle.net/10568/89049) redirects incorrectly
- I had mentioned this to Maria and Francesca a few months ago but it seems to never have been resolved
- The `dspace cleanup -v` finally finished after a few days of running and stopping...
- I decided to update the thumbnails in the Bioversity books collection because I saw a few old ones suffering from the CropBox issue
- Also, all day there's been a high load on CGSpace, with lots of locks in PostgreSQL
- I had been waiting until the bitstream cleanup finished... now I might need to restart PostgreSQL to kill some old locks as something needs to give
- I restarted PostgreSQL, but DSpace was still hanging on simple XMLUI options so I ended up restarting Tomcat
- Tag 544 ORCID identifiers with my script
- I updated my `generation-loss.sh` and `improved-dspace-thumbnails` scripts to include thirty-five PDFs from CGSpace (up from twenty-four) to get a larger sample
- Now starting to get some numbers comparing JPEG, WebP, and AVIF
- First, out of curiousity, I checked the average ssimulacra2 scores at Q75, Q80, and Q92 for each format:
| | Q75 | Q80 | Q92 |
|------|-----|-----|-----|
| JPEG | 70 | 73 | 88 |
| WebP | 73 | 76 | 82 |
| AVIF | 82 | 83 | 92 |
- Then I checked the quality and file size (bytes) needed to hit an average ssimulacra2 score of 80 with each format:
- **JPEG**: Q89, 124596 bytes
- **WebP**: Q88, 84935 bytes (32% smaller than JPEG size)
- **AVIF**: Q62, 60347 bytes (52% smaller than JPEG size)
- [Google's original WebP study](https://developers.google.com/speed/webp/docs/webp_study) uses this technique to compare WebP to JPEG too
- As the quality settings are not comparable between formats, we need to compare the formats at matching perceptual scores (ssimulacra2 in this case)
- I used a ssimulacra2 score of 80 because that's the about the highest score I see with WebP using my samples, though JPEG and AVIF do go higher
- Also, according to current ssimulacra2 (v2.1), a score of 70 is "high quality" and a score of 90 is "very high quality", so 80 should be reasonably high enough...
- Export CGSpace to check for missing Initiatives mappings
<!-- vim: set sw=2 ts=2: -->

4
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@ -20,7 +20,7 @@ I filed an issue to ask about Java 11&#43; support
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-10/" />
<meta property="article:published_time" content="2022-10-01T19:45:36+03:00" />
<meta property="article:modified_time" content="2022-10-31T16:59:47+03:00" />
<meta property="article:modified_time" content="2023-04-18T11:08:15-07:00" />
@ -48,7 +48,7 @@ I filed an issue to ask about Java 11&#43; support
"url": "https://alanorth.github.io/cgspace-notes/2022-10/",
"wordCount": "3768",
"datePublished": "2022-10-01T19:45:36+03:00",
"dateModified": "2022-10-31T16:59:47+03:00",
"dateModified": "2023-04-18T11:08:15-07:00",
"author": {
"@type": "Person",
"name": "Alan Orth"

89
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@ -20,7 +20,7 @@ Start a harvest on AReS
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-04/" />
<meta property="article:published_time" content="2023-04-02T08:19:36+03:00" />
<meta property="article:modified_time" content="2023-04-06T16:13:30+03:00" />
<meta property="article:modified_time" content="2023-04-18T11:08:15-07:00" />
@ -46,9 +46,9 @@ Start a harvest on AReS
"@type": "BlogPosting",
"headline": "April, 2023",
"url": "https://alanorth.github.io/cgspace-notes/2023-04/",
"wordCount": "1556",
"wordCount": "1970",
"datePublished": "2023-04-02T08:19:36+03:00",
"dateModified": "2023-04-06T16:13:30+03:00",
"dateModified": "2023-04-18T11:08:15-07:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -573,8 +573,11 @@ Start a harvest on AReS
</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>$ psql -d dspace -c <span style="color:#e6db74">&#34;update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (&#39;a7ddf477-1c04-4de0-9c7a-4d3c84a875bc&#39;, &#39;9582b661-9c2d-4c86-be22-c3b0942b646a&#39;, &#39;210a4d5d-3af9-46f0-84cc-682dd1431762&#39;)&#34;</span>
</span></span></code></pre></div><h2 id="2023-04-18">2023-04-18</h2>
<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>$ psql -d dspace -c <span style="color:#e6db74">&#34;update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (&#39;a7ddf477-1c04-4de0-9c7a-4d3c84a875bc&#39;, &#39;9582b661-9c2d-4c86-be22-c3b0942b646a&#39;, &#39;210a4d5d-3af9-46f0-84cc-682dd1431762&#39;, &#39;51115f07-0a60-4988-8536-b9ebd2a5e15e&#39;, &#39;0fc5021d-3264-413a-b2e2-74bda38a394e&#39;, &#39;4704fa62-b8ab-4dfe-b7aa-0e4905f8412a&#39;)&#34;</span>
</span></span></code></pre></div><ul>
<li>This process ended up taking a few days because each iteration ran for over four hours before failing on the next UUID, sighhhhh</li>
</ul>
<h2 id="2023-04-18">2023-04-18</h2>
<ul>
<li>Regarding the item Abenet noticed yesterday that has a blank page and a nullPointerException
<ul>
@ -584,6 +587,82 @@ Start a harvest on AReS
</ul>
</li>
</ul>
<h2 id="2023-04-19">2023-04-19</h2>
<ul>
<li>I fixed the Bioversity item by deleting the <code>9781138781276.jpg</code> bitstream via the REST API
<ul>
<li>I <em>think</em> Francesca might have changed the &ldquo;format&rdquo; of it?</li>
<li>Anyway, this item has a PDF so we have a proper thumbnail and don&rsquo;t need that other journal cover one</li>
</ul>
</li>
<li>I noticed a URL for this <a href="https://hdl.handle.net/10568/89049">Bioversity item</a> redirects incorrectly
<ul>
<li>I had mentioned this to Maria and Francesca a few months ago but it seems to never have been resolved</li>
</ul>
</li>
<li>The <code>dspace cleanup -v</code> finally finished after a few days of running and stopping&hellip;</li>
<li>I decided to update the thumbnails in the Bioversity books collection because I saw a few old ones suffering from the CropBox issue</li>
<li>Also, all day there&rsquo;s been a high load on CGSpace, with lots of locks in PostgreSQL
<ul>
<li>I had been waiting until the bitstream cleanup finished&hellip; now I might need to restart PostgreSQL to kill some old locks as something needs to give</li>
<li>I restarted PostgreSQL, but DSpace was still hanging on simple XMLUI options so I ended up restarting Tomcat</li>
</ul>
</li>
<li>Tag 544 ORCID identifiers with my script</li>
<li>I updated my <code>generation-loss.sh</code> and <code>improved-dspace-thumbnails</code> scripts to include thirty-five PDFs from CGSpace (up from twenty-four) to get a larger sample
<ul>
<li>Now starting to get some numbers comparing JPEG, WebP, and AVIF</li>
<li>First, out of curiousity, I checked the average ssimulacra2 scores at Q75, Q80, and Q92 for each format:</li>
</ul>
</li>
</ul>
<table>
<thead>
<tr>
<th></th>
<th>Q75</th>
<th>Q80</th>
<th>Q92</th>
</tr>
</thead>
<tbody>
<tr>
<td>JPEG</td>
<td>70</td>
<td>73</td>
<td>88</td>
</tr>
<tr>
<td>WebP</td>
<td>73</td>
<td>76</td>
<td>82</td>
</tr>
<tr>
<td>AVIF</td>
<td>82</td>
<td>83</td>
<td>92</td>
</tr>
</tbody>
</table>
<ul>
<li>Then I checked the quality and file size (bytes) needed to hit an average ssimulacra2 score of 80 with each format:
<ul>
<li><strong>JPEG</strong>: Q89, 124596 bytes</li>
<li><strong>WebP</strong>: Q88, 84935 bytes (32% smaller than JPEG size)</li>
<li><strong>AVIF</strong>: Q62, 60347 bytes (52% smaller than JPEG size)</li>
</ul>
</li>
<li><a href="https://developers.google.com/speed/webp/docs/webp_study">Google&rsquo;s original WebP study</a> uses this technique to compare WebP to JPEG too
<ul>
<li>As the quality settings are not comparable between formats, we need to compare the formats at matching perceptual scores (ssimulacra2 in this case)</li>
<li>I used a ssimulacra2 score of 80 because that&rsquo;s the about the highest score I see with WebP using my samples, though JPEG and AVIF do go higher</li>
<li>Also, according to current ssimulacra2 (v2.1), a score of 70 is &ldquo;high quality&rdquo; and a score of 90 is &ldquo;very high quality&rdquo;, so 80 should be reasonably high enough&hellip;</li>
</ul>
</li>
<li>Export CGSpace to check for missing Initiatives mappings</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:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2023-04-06T16:13:30+03:00" />
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