CGSpace Notes

2022-11-01

• Last night I re-synced DSpace 7 Test from CGSpace
  • I also updated all my local 7_x-dev branches on the latest upstreams
• I spent some time updating the authorizations in Alliance collections
  • I want to make sure they use groups instead of individuals where possible!
• I reverted the Cocoon autosave change because it was more of a nuissance that Peter can’t upload CSVs from the web interface and is a very low severity security issue

• I ran FixLowQualityThumbnails from cgspace-java-helpers on some large collections on CGSpace and ended up fixing 194 items!
• I did some minor checking and uploaded twenty-four IFPRI outputs for the Initiatives to DSpace Test
• Tim merged my pull request to override the ImageMagick PDF density in DSpace 7
  • 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:

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:

$ 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:

$ 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:

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…

$ 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”:

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:

$ 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 on the iso-3166-1 npm package to update the name of Turkey to Türkiye
  • I also filed an issue and a pull request on the pycountry package
  • I also filed an issue and a pull request 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 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”
• Port the ImageMagick PDF cropbox fix 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:

$ 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