alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-22 06:35:03 +01:00
Code Issues Projects Releases Wiki Activity

Add notes for 2021-08-11

Browse Source
This commit is contained in:
Alan Orth 2021-08-11 16:19:26 +03:00
parent 33d5d98502
commit dba953ae9b
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
25 changed files with 118 additions and 31 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

40
content/posts/2021-08.md
View File

@ -210,6 +210,7 @@ if(cells['sherpa romeo journal title'].value == cells['crossref journal title'].
- It is faster and uses less memory than GraphicsMagick (and ImageMagick), and produces nice thumbnails from PDFs
- One drawback is that libvips uses Poppler instead of Graphicsmagick, which apparently means that it can't work in CMYK
- I tested one item (10568/51999) that uses CMYK and the thumbnail looked OK (closer to the original than GraphicsMagick), so I'm not sure...
- Perhaps this is not a problem after all, see this PR from 2019: https://github.com/libvips/libvips/pull/1196
- I did some tests of the memory used and time elapsed with libvips, GraphicsMagick, and ImageMagick:
```console
@ -225,5 +226,42 @@ $ /usr/bin/time -f %M:%e convert -auto-orient /tmp/impdfthumb2862933674765647409
- The ImageMagick way is the same as how DSpace does it (first creating an intermediary image, then getting a thumbnail)
- libvips does use less time and memory... I should do more tests!
- I wonder if I can try to use these [unofficial Java bindings](https://github.com/criteo/JVips/blob/master/src/test/java/com/criteo/vips/example/SimpleExample.java) in DSpace
- The authors of the JVips project wrote a nice blog post about libvips performance: https://medium.com/criteo-engineering/boosting-image-processing-performance-from-imagemagick-to-libvips-268cc3451d55
- Ouch, JVips is Java 8 only as far as I can tell... that works now, but it's a non-starter going forward
<!-- vim: set sw=2 ts=2: -->
## 2021-08-11
- Peter got back to me about the journal title cleanup
- From his corrections it seems an overwhelming majority of his choices match the Sherpa Romeo version of the titles rather than Crossref's
- Anyways, I exported the originals that were the same in Sherpa Romeo and Crossref as well as Peter's selections for where Sherpa Romeo and Crossref differred:
```console
$ csvcut -c cgspace ~/Downloads/2021-08-09-CGSpace-Journals-PB.csv | sort -u | sed 1d > /tmp/journals1.txt
$ csvcut -c 'sherpa romeo journal title' ~/Downloads/2021-08-09-CGSpace-Journals-All.csv | sort -u | sed 1d > /tmp/journals2.txt
$ cat /tmp/journals1.txt /tmp/journals2.txt | sort -u | wc -l
1911
```
- Now I will create a controlled vocabulary out of this list and reconcile our existing journal title metadata with it in OpenRefine
- I exported a list of all the journal titles we have in the `cg.journal` field:
```console
localhost/dspace63= > \COPY (SELECT DISTINCT(text_value) AS "cg.journal" FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (251)) to /tmp/2021-08-11-journals.csv WITH CSV;
COPY 3245
```
- I started looking at reconciling them with reconcile-csv in OpenRefine, but ouch, there are 1,600 journal titles that don't match, so I'd have to go check many of them manually before selecting a match or fixing them...
- I think it's better if I try to write a Python script to fetch the ISSNs for each journal article and update them that way
- Or instead of doing it via SQL I could use CSV and parse the values there...
- A few more issues:
- Some ISSNs are non-existent in Sherpa Romeo and Crossref, but appear on issn.org's web search (their API is invite only)
- Some titles are different across all three datasets, for example ISSN 0003-1305:
- [According to ISSN.org](https://portal.issn.org/resource/ISSN/0003-1305) this is "The American statistician"
- [According to Sherpa Romeo](https://v2.sherpa.ac.uk/id/publication/20807) this is "American Statistician"
- [According to Crossref](https://search.crossref.org/?q=0003-1305&from_ui=yes&container-title=The+American+Statistician) this is "The American Statistician"
- I also realized that our previous controlled vocabulary came from CGSpace's top 500 journals, so when I replaced it with the generated list earlier today we lost some journals
- Now I went back and merged the previous with the new, and manually removed duplicates (sigh)
- I requested access to the issn.org OAI-PMH API so I can use their registry...
<!-- v[im: set sw=2 ts=2: -->

55
docs/2021-08/index.html
View File

@ -18,7 +18,7 @@ I decided to upgrade linode20 from Ubuntu 18.04 to 20.04
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2021-08/" />
<meta property="article:published_time" content="2021-08-01T09:01:07+03:00" />
<meta property="article:modified_time" content="2021-08-09T17:10:45+03:00" />
<meta property="article:modified_time" content="2021-08-09T17:34:13+03:00" />
@ -42,9 +42,9 @@ I decided to upgrade linode20 from Ubuntu 18.04 to 20.04
"@type": "BlogPosting",
"headline": "August, 2021",
"url": "https://alanorth.github.io/cgspace-notes/2021-08/",
"wordCount": "1636",
"wordCount": "2059",
"datePublished": "2021-08-01T09:01:07+03:00",
"dateModified": "2021-08-09T17:10:45+03:00",
"dateModified": "2021-08-09T17:34:13+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -327,6 +327,7 @@ $ csvjoin -c issn /tmp/2021-08-09-journals-sherpa-romeo.csv /tmp/2021-08-09-jour
<li>It is faster and uses less memory than GraphicsMagick (and ImageMagick), and produces nice thumbnails from PDFs</li>
<li>One drawback is that libvips uses Poppler instead of Graphicsmagick, which apparently means that it can&rsquo;t work in CMYK</li>
<li>I tested one item (10568/51999) that uses CMYK and the thumbnail looked OK (closer to the original than GraphicsMagick), so I&rsquo;m not sure&hellip;</li>
<li>Perhaps this is not a problem after all, see this PR from 2019: <a href="https://github.com/libvips/libvips/pull/1196">https://github.com/libvips/libvips/pull/1196</a></li>
</ul>
</li>
<li>I did some tests of the memory used and time elapsed with libvips, GraphicsMagick, and ImageMagick:</li>
@ -343,6 +344,54 @@ $ /usr/bin/time -f %M:%e convert -auto-orient /tmp/impdfthumb2862933674765647409
<li>The ImageMagick way is the same as how DSpace does it (first creating an intermediary image, then getting a thumbnail)
<ul>
<li>libvips does use less time and memory&hellip; I should do more tests!</li>
<li>I wonder if I can try to use these <a href="https://github.com/criteo/JVips/blob/master/src/test/java/com/criteo/vips/example/SimpleExample.java">unofficial Java bindings</a> in DSpace</li>
<li>The authors of the JVips project wrote a nice blog post about libvips performance: <a href="https://medium.com/criteo-engineering/boosting-image-processing-performance-from-imagemagick-to-libvips-268cc3451d55">https://medium.com/criteo-engineering/boosting-image-processing-performance-from-imagemagick-to-libvips-268cc3451d55</a></li>
<li>Ouch, JVips is Java 8 only as far as I can tell&hellip; that works now, but it&rsquo;s a non-starter going forward</li>
</ul>
</li>
</ul>
<h2 id="2021-08-11">2021-08-11</h2>
<ul>
<li>Peter got back to me about the journal title cleanup
<ul>
<li>From his corrections it seems an overwhelming majority of his choices match the Sherpa Romeo version of the titles rather than Crossref&rsquo;s</li>
<li>Anyways, I exported the originals that were the same in Sherpa Romeo and Crossref as well as Peter&rsquo;s selections for where Sherpa Romeo and Crossref differred:</li>
</ul>
</li>
</ul>
<pre><code class="language-console" data-lang="console">$ csvcut -c cgspace ~/Downloads/2021-08-09-CGSpace-Journals-PB.csv | sort -u | sed 1d &gt; /tmp/journals1.txt
$ csvcut -c 'sherpa romeo journal title' ~/Downloads/2021-08-09-CGSpace-Journals-All.csv | sort -u | sed 1d &gt; /tmp/journals2.txt
$ cat /tmp/journals1.txt /tmp/journals2.txt | sort -u | wc -l
1911
</code></pre><ul>
<li>Now I will create a controlled vocabulary out of this list and reconcile our existing journal title metadata with it in OpenRefine</li>
<li>I exported a list of all the journal titles we have in the <code>cg.journal</code> field:</li>
</ul>
<pre><code class="language-console" data-lang="console">localhost/dspace63= &gt; \COPY (SELECT DISTINCT(text_value) AS &quot;cg.journal&quot; FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (251)) to /tmp/2021-08-11-journals.csv WITH CSV;
COPY 3245
</code></pre><ul>
<li>I started looking at reconciling them with reconcile-csv in OpenRefine, but ouch, there are 1,600 journal titles that don&rsquo;t match, so I&rsquo;d have to go check many of them manually before selecting a match or fixing them&hellip;
<ul>
<li>I think it&rsquo;s better if I try to write a Python script to fetch the ISSNs for each journal article and update them that way</li>
<li>Or instead of doing it via SQL I could use CSV and parse the values there&hellip;</li>
</ul>
</li>
<li>A few more issues:
<ul>
<li>Some ISSNs are non-existent in Sherpa Romeo and Crossref, but appear on issn.org&rsquo;s web search (their API is invite only)</li>
<li>Some titles are different across all three datasets, for example ISSN 0003-1305:
<ul>
<li><a href="https://portal.issn.org/resource/ISSN/0003-1305">According to ISSN.org</a> this is &ldquo;The American statistician&rdquo;</li>
<li><a href="https://v2.sherpa.ac.uk/id/publication/20807">According to Sherpa Romeo</a> this is &ldquo;American Statistician&rdquo;</li>
<li><a href="https://search.crossref.org/?q=0003-1305&amp;from_ui=yes&amp;container-title=The+American+Statistician">According to Crossref</a> this is &ldquo;The American Statistician&rdquo;</li>
</ul>
</li>
</ul>
</li>
<li>I also realized that our previous controlled vocabulary came from CGSpace&rsquo;s top 500 journals, so when I replaced it with the generated list earlier today we lost some journals
<ul>
<li>Now I went back and merged the previous with the new, and manually removed duplicates (sigh)</li>
<li>I requested access to the issn.org OAI-PMH API so I can use their registry&hellip;</li>
</ul>
</li>
</ul>

2
docs/categories/index.html
View File

@ -10,7 +10,7 @@
<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="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/categories/notes/index.html
View File

@ -10,7 +10,7 @@
<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/notes/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/categories/notes/page/2/index.html
View File

@ -10,7 +10,7 @@
<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/notes/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/categories/notes/page/3/index.html
View File

@ -10,7 +10,7 @@
<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/notes/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/categories/notes/page/4/index.html
View File

@ -10,7 +10,7 @@
<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/notes/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/categories/notes/page/5/index.html
View File

@ -10,7 +10,7 @@
<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/notes/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/2/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/3/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/4/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/5/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/6/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/7/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/page/8/index.html
View File

@ -10,7 +10,7 @@
<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/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/2/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/3/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/4/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/5/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/6/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/7/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

2
docs/posts/page/8/index.html
View File

@ -10,7 +10,7 @@
<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/posts/" />
<meta property="og:updated_time" content="2021-08-09T17:10:45+03:00" />
<meta property="og:updated_time" content="2021-08-09T17:34:13+03:00" />

10
docs/sitemap.xml
View File

@ -3,19 +3,19 @@
xmlns:xhtml="http://www.w3.org/1999/xhtml">
<url>
<loc>https://alanorth.github.io/cgspace-notes/2021-08/</loc>
<lastmod>2021-08-09T17:10:45+03:00</lastmod>
<lastmod>2021-08-09T17:34:13+03:00</lastmod>
</url><url>
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
<lastmod>2021-08-09T17:10:45+03:00</lastmod>
<lastmod>2021-08-09T17:34:13+03:00</lastmod>
</url><url>
<loc>https://alanorth.github.io/cgspace-notes/</loc>
<lastmod>2021-08-09T17:10:45+03:00</lastmod>
<lastmod>2021-08-09T17:34:13+03:00</lastmod>
</url><url>
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
<lastmod>2021-08-09T17:10:45+03:00</lastmod>
<lastmod>2021-08-09T17:34:13+03:00</lastmod>
</url><url>
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
<lastmod>2021-08-09T17:10:45+03:00</lastmod>
<lastmod>2021-08-09T17:34:13+03:00</lastmod>
</url><url>
<loc>https://alanorth.github.io/cgspace-notes/2021-07/</loc>
<lastmod>2021-08-01T16:19:05+03:00</lastmod>