Add notes for 2023-04-06

content/posts/2023-04.md

@@ -14,4 +14,81 @@ categories: ["Notes"]
 
 <!--more-->
 
+- I'm starting to get annoyed at my shell script for doing ImageMagick tests and looking to re-write it in something object oriented like Python
+  - There doesn't seem to be an official ImageMagick Python binding on pypi.org, perhaps I can use [Wand](https://docs.wand-py.org)?
+- Testing Wand in Python:
+
+```python
+from wand.image import Image
+
+with Image(filename='data/10568-103447.pdf[0]', resolution=144) as first_page:
+    print(first_page.height)
+```
+
+- I spent more time re-working my thumbnail scripts to compare the resized images and other minor changes
+  - I am realizing that doing the thumbnails directly from the source improves the ssimulacra2 score by 1-3% points compared to DSpace's method of creating a lossy supersample followed by a lossy resized thumbnail
+
+## 2023-04-03
+
+- The harvest on AReS that I started yesterday never finished, and actually seems to have died...
+  - Also, Fabio and Patrizio from Alliance emailed me to ask if there is something wrong with the REST API because they are having problems
+  - I stopped the harvest and started the plugins to get the remaining items via the sitemap...
+
+## 2023-04-04
+
+- Presentation about CGSpace metadata, controlled vocabularies, and curation to Pooja's communications and development team at UNEP
+  - I uploaded the presentation to CGSpace here: https://hdl.handle.net/10568/129896
+- Someone from the system organization contacted me to ask how to download a few thousand PDFs from a spreadsheet with DOIs and Handles
+
+```console
+$ csvcut -c Handle ~/Downloads/2023-04-04-Donald.csv \
+    | sed \
+        -e 1d \
+        -e 's_https://hdl.handle.net/__' \
+        -e 's_https://cgspace.cgiar.org/handle/__' \
+        -e 's_http://hdl.handle.net/__' \
+    | sort -u > /tmp/handles.txt
+```
+
+- Then I used the `get_dspace_pdfs.py` script to download them
+
+## 2023-04-05
+
+- After some cleanup on Donald's DOIs I started the `get_scihub_pdfs.py` script
+
+## 2023-04-06
+
+- I did some more work to cleanup and streamline my next generation of DSpace thumbnail testing scripts
+  - I think I found a bug in ImageMagick 7.1.1.5 where CMYK to sRGB conversion fails if we use image operations like `-density` or `-define` before reading the input file
+  - I started [a discussion on the ImageMagick GitHub](https://github.com/ImageMagick/ImageMagick/discussions/6234) to ask
+- Yesterday I started downloading the rest of the PDFs from Donald, those that had DOIs
+  - As a measure of caution, I extracted the list of DOIs and used my `crossref_doi_lookup.py` script to get their licenses from Crossref:
+
+```console
+$ ./ilri/crossref_doi_lookup.py -e xxxx@i.org -i /tmp/dois.txt -o /tmp/donald-crossref-dois.csv -d
+```
+
+- Then I did some CSV manipulation to extract the DOIs that were Creative Commons licensed, excluding any that were "No Derivatives", and re-formatting the DOIs:
+
+```console
+$ csvcut -c doi,license /tmp/donald-crossref-dois.csv \
+  | csvgrep -c license -m 'creativecommons' \
+  | csvgrep -c license -i -r 'by-(nd|nc-nd)' \
+  | sed -e 's_^10_https://doi.org/10_' \
+    -e 's/\(am\|tdm\|unspecified\|vor\): //' \
+  | tee /tmp/donald-open-dois.csv \
+  | wc -l
+4268
+```
+
+- From those I filtered for the DOIs for which I had downloaded PDFs, in the `filename` column of the Sci-Hub script and copied them to a separate directory:
+
+```console
+$ for file in $(csvjoin -c doi /tmp/donald-doi-pdfs.csv /tmp/donald-open-dois.csv | csvgrep -c filename -i -r '^$' | csvcut -c filename | sed 1d); do cp --reflink=always "$file" "creative-commons-licensed/$file"; done
+```
+
+- I used BTRFS copy-on-write via reflinks to make sure I didn't duplicate the files :-D
+- I ran out of time and had to stop the process around 3,127 PDFs
+  - I zipped them up and sent them to the others, along with a CSV of the DOIs, PDF filenames, and licenses
+
 <!-- vim: set sw=2 ts=2: -->

docs/2023-03/index.html

@@ -16,7 +16,7 @@ I finally got through with porting the input form from DSpace 6 to DSpace 7
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-03/" />
 <meta property="article:published_time" content="2023-03-01T07:58:36+03:00" />
-<meta property="article:modified_time" content="2023-03-30T16:59:20+03:00" />
+<meta property="article:modified_time" content="2023-04-02T09:16:25+03:00" />
 
 
 
@@ -40,7 +40,7 @@ I finally got through with porting the input form from DSpace 6 to DSpace 7
   "url": "https://alanorth.github.io/cgspace-notes/2023-03/",
   "wordCount": "4810",
   "datePublished": "2023-03-01T07:58:36+03:00",
-  "dateModified": "2023-03-30T16:59:20+03:00",
+  "dateModified": "2023-04-02T09:16:25+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"

docs/2023-04/index.html

@@ -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="2023-04-02T08:19:36+03:00" />
+<meta property="article:modified_time" content="2023-04-02T09:16:25+03:00" />
 
 
 
@@ -46,9 +46,9 @@ Start a harvest on AReS
   "@type": "BlogPosting",
   "headline": "April, 2023",
   "url": "https://alanorth.github.io/cgspace-notes/2023-04/",
-  "wordCount": "39",
+  "wordCount": "569",
   "datePublished": "2023-04-02T08:19:36+03:00",
-  "dateModified": "2023-04-02T08:19:36+03:00",
+  "dateModified": "2023-04-02T09:16:25+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -132,6 +132,95 @@ Start a harvest on AReS
 </li>
 <li>Start a harvest on AReS</li>
 </ul>
+<ul>
+<li>I&rsquo;m starting to get annoyed at my shell script for doing ImageMagick tests and looking to re-write it in something object oriented like Python
+<ul>
+<li>There doesn&rsquo;t seem to be an official ImageMagick Python binding on pypi.org, perhaps I can use <a href="https://docs.wand-py.org">Wand</a>?</li>
+</ul>
+</li>
+<li>Testing Wand in Python:</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">from</span> wand.image <span style="color:#f92672">import</span> Image
+</span></span><span style="display:flex;"><span>
+</span></span><span style="display:flex;"><span><span style="color:#66d9ef">with</span> Image(filename<span style="color:#f92672">=</span><span style="color:#e6db74">&#39;data/10568-103447.pdf[0]&#39;</span>, resolution<span style="color:#f92672">=</span><span style="color:#ae81ff">144</span>) <span style="color:#66d9ef">as</span> first_page:
+</span></span><span style="display:flex;"><span>    print(first_page<span style="color:#f92672">.</span>height)
+</span></span></code></pre></div><ul>
+<li>I spent more time re-working my thumbnail scripts to compare the resized images and other minor changes
+<ul>
+<li>I am realizing that doing the thumbnails directly from the source improves the ssimulacra2 score by 1-3% points compared to DSpace&rsquo;s method of creating a lossy supersample followed by a lossy resized thumbnail</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-04-03">2023-04-03</h2>
+<ul>
+<li>The harvest on AReS that I started yesterday never finished, and actually seems to have died&hellip;
+<ul>
+<li>Also, Fabio and Patrizio from Alliance emailed me to ask if there is something wrong with the REST API because they are having problems</li>
+<li>I stopped the harvest and started the plugins to get the remaining items via the sitemap&hellip;</li>
+</ul>
+</li>
+</ul>
+<h2 id="2023-04-04">2023-04-04</h2>
+<ul>
+<li>Presentation about CGSpace metadata, controlled vocabularies, and curation to Pooja&rsquo;s communications and development team at UNEP
+<ul>
+<li>I uploaded the presentation to CGSpace here: <a href="https://hdl.handle.net/10568/129896">https://hdl.handle.net/10568/129896</a></li>
+</ul>
+</li>
+<li>Someone from the system organization contacted me to ask how to download a few thousand PDFs from a spreadsheet with DOIs and Handles</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 Handle ~/Downloads/2023-04-04-Donald.csv <span style="color:#ae81ff">\
+</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span>    | sed \
+</span></span><span style="display:flex;"><span>        -e 1d \
+</span></span><span style="display:flex;"><span>        -e &#39;s_https://hdl.handle.net/__&#39; \
+</span></span><span style="display:flex;"><span>        -e &#39;s_https://cgspace.cgiar.org/handle/__&#39; \
+</span></span><span style="display:flex;"><span>        -e &#39;s_http://hdl.handle.net/__&#39; \
+</span></span><span style="display:flex;"><span>    | sort -u &gt; /tmp/handles.txt
+</span></span></code></pre></div><ul>
+<li>Then I used the <code>get_dspace_pdfs.py</code> script to download them</li>
+</ul>
+<h2 id="2023-04-05">2023-04-05</h2>
+<ul>
+<li>After some cleanup on Donald&rsquo;s DOIs I started the <code>get_scihub_pdfs.py</code> script</li>
+</ul>
+<h2 id="2023-04-06">2023-04-06</h2>
+<ul>
+<li>I did some more work to cleanup and streamline my next generation of DSpace thumbnail testing scripts
+<ul>
+<li>I think I found a bug in ImageMagick 7.1.1.5 where CMYK to sRGB conversion fails if we use image operations like <code>-density</code> or <code>-define</code> before reading the input file</li>
+<li>I started <a href="https://github.com/ImageMagick/ImageMagick/discussions/6234">a discussion on the ImageMagick GitHub</a> to ask</li>
+</ul>
+</li>
+<li>Yesterday I started downloading the rest of the PDFs from Donald, those that had DOIs
+<ul>
+<li>As a measure of caution, I extracted the list of DOIs and used my <code>crossref_doi_lookup.py</code> script to get their licenses from Crossref:</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>$ ./ilri/crossref_doi_lookup.py -e xxxx@i.org -i /tmp/dois.txt -o /tmp/donald-crossref-dois.csv -d
+</span></span></code></pre></div><ul>
+<li>Then I did some CSV manipulation to extract the DOIs that were Creative Commons licensed, excluding any that were &ldquo;No Derivatives&rdquo;, and re-formatting the DOIs:</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 doi,license /tmp/donald-crossref-dois.csv <span style="color:#ae81ff">\
+</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span>  | csvgrep -c license -m &#39;creativecommons&#39; \
+</span></span><span style="display:flex;"><span>  | csvgrep -c license -i -r &#39;by-(nd|nc-nd)&#39; \
+</span></span><span style="display:flex;"><span>  | sed -e &#39;s_^10_https://doi.org/10_&#39; \
+</span></span><span style="display:flex;"><span>    -e &#39;s/\(am\|tdm\|unspecified\|vor\): //&#39; \
+</span></span><span style="display:flex;"><span>  | tee /tmp/donald-open-dois.csv \
+</span></span><span style="display:flex;"><span>  | wc -l
+</span></span><span style="display:flex;"><span>4268
+</span></span></code></pre></div><ul>
+<li>From those I filtered for the DOIs for which I had downloaded PDFs, in the <code>filename</code> column of the Sci-Hub script and copied them to a separate directory:</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">for</span> file in <span style="color:#66d9ef">$(</span>csvjoin -c doi /tmp/donald-doi-pdfs.csv /tmp/donald-open-dois.csv | csvgrep -c filename -i -r <span style="color:#e6db74">&#39;^$&#39;</span> | csvcut -c filename | sed 1d<span style="color:#66d9ef">)</span>; <span style="color:#66d9ef">do</span> cp --reflink<span style="color:#f92672">=</span>always <span style="color:#e6db74">&#34;</span>$file<span style="color:#e6db74">&#34;</span> <span style="color:#e6db74">&#34;creative-commons-licensed/</span>$file<span style="color:#e6db74">&#34;</span>; <span style="color:#66d9ef">done</span>
+</span></span></code></pre></div><ul>
+<li>I used BTRFS copy-on-write via reflinks to make sure I didn&rsquo;t duplicate the files :-D</li>
+<li>I ran out of time and had to stop the process around 3,127 PDFs
+<ul>
+<li>I zipped them up and sent them to the others, along with a CSV of the DOIs, PDF filenames, and licenses</li>
+</ul>
+</li>
+</ul>
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