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
+
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