cgspace-notes/content/posts/2022-12.md

title	date	author	categories
December, 2022	2022-12-01T08:52:36+03:00	Alan Orth	Notes

2022-12-01

• Fix some incorrect regions on CGSpace
  • I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions
• Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!
• Replace "East Asia" with "Eastern Asia" region on CGSpace (UN M.49 region)

• CGSpace and PRMS information session with Enrico and a bunch of researchers
• I noticed some minor issues with SPDX licenses and AGROVOC terms in items submitted by TIP so I sent a message to Daniel from Alliance
• I startd a harvest on AReS since we've updated so much metadata recently

2022-12-02

• File some issues related to metadata on the MEL issue tracker
  • Only use "Open Access" or "Limited Access" access rights when publishing items on CGSpace
  • Set the description when submitting bitstreams to CGSpace
  • Some items have a Creative Commons license, but are Limited Access and bitstreams are locked

2022-12-03

• I downloaded a fresh copy of CLARISA's institutions list as well as ROR's latest dump from 2022-12-01 to check how many are matching:

$ curl -s https://api.clarisa.cgiar.org/api/institutions | json_pp > ~/Downloads/2022-12-03-CLARISA-institutions.json
$ jq -r '.[] | .name' ~/Downloads/2022-12-03-CLARISA-institutions.json > ~/Downloads/2022-12-03-CLARISA-institutions.txt
$ ./ilri/ror-lookup.py -i ~/Downloads/2022-12-03-CLARISA-institutions.txt -o /tmp/clarisa-ror-matches.csv -r v1.15-2022-12-01-ror-data.json
$ csvgrep -c matched -m true /tmp/clarisa-ror-matches.csv | wc -l
1864
$ wc -l ~/Downloads/2022-12-03-CLARISA-institutions.txt
7060 /home/aorth/Downloads/2022-12-03-CLARISA-institutions.txt

• Out of the box they match 26.4%, but there are many institutions with multiple languages in the text value, as well as countries in parentheses so I think it could be higher
• If I replace the slashes and remove the countries at the end there are slightly more matches, around 29%:

$ sed -e 's_ / _\n_' -e 's_/_\n_' -e 's/ \?(.*)$//' ~/Downloads/2022-12-03-CLARISA-institutions.txt > ~/Downloads/2022-12-03-CLARISA-institutions-alan.txt

• I checked CGSpace's top 1,000 affiliations too, first exporting from PostgreSQL:

localhost/dspacetest= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1000) to /tmp/2022-11-22-affiliations.csv;

• Then cutting (tab is the default delimeter):

$ cut -f 1 /tmp/2022-11-22-affiliations.csv > 2022-11-22-affiliations.txt
$ ./ilri/ror-lookup.py -i 2022-11-22-affiliations.txt -o /tmp/cgspace-matches.csv -r v1.15-2022-12-01-ror-data.json
$ csvgrep -c matched -m true /tmp/cgspace-matches.csv | wc -l
542

• So that's a 54% match for our top affiliations
• I realized we should actually check affiliations and sponsors, since those are stored in separate fields
  • When I add those the matches go down a bit to 45%
• Oh man, I realized institutions like Université d'Abomey Calavi don't match in ROR because they are like this in the JSON:

"name": "Universit\u00e9 d'Abomey-Calavi"

• So we likely match a bunch more than 50%...
• I exported a list of affiliations and donors from CGSpace for Peter to look over and send corrections

2022-12-05

• First day of PRMS technical workshop in Rome
• Last night I submitted a CSV import with changes to 1,500 Alliance items (adding regions) and it hadn't completed after twenty-four hours so I canceled it
  • Not sure if there is some rollback that will happen or what state the database will be in, so I will wait a few hours to see what happens before trying to modify those items again
  • I started it again a few hours later with a subset of the items and 4GB of RAM instead of 2
  • It completed successfully...

2022-12-07

• I found a bug in my csv-metadata-quality script regarding the regions
  • I was accidentally checking cg.coverage.subregion due to a sloppy regex
  • This means I've added a few thousand UN M.49 regions to the cg.coverage.subregion field in the last few days
  • I had to extract them from CGSpace and delete them using delete-metadata-values.py
• My DSpace 7.x pull request to tell ImageMagick about the PDF CropBox was merged
• Start a harvest on AReS

2022-12-08

• While on the plane I decided to fix some ORCID identifiers, as I had seen some poorly formatted ones
  • I couldn't remember the XPath syntax so this was kinda ghetto:

$ xmllint --xpath '//node/isComposedBy/node()' dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep -oE 'label=".*"' | sed -e 's/label="//' -e 's/"$//' > /tmp/orcid-names.txt
$ ./ilri/update-orcids.py -i /tmp/orcid-names.txt -db dspace -u dspace -p 'fuuu' -m 247

• After that there were still some poorly formatted ones that my script didn't fix, so perhaps these are new ones not in our list
  • I dumped them and combined with the existing ones to resolve later:

localhost/dspace= ☘ \COPY (SELECT dspace_object_id,text_value FROM metadatavalue WHERE metadata_field_id=247 AND text_value LIKE '%http%') to /tmp/orcid-formatting.txt;
COPY 36

• I think there are really just some new ones...

$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/orcid-formatting.txt| grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2022-12-08-orcids.txt 
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u | wc -l
1907
$ wc -l /tmp/2022-12-08-orcids.txt
1939 /tmp/2022-12-08-orcids.txt

• Then I applied these updates on CGSpace
• Maria mentioned that she was getting a lot more items in her daily subscription emails
  • I had a hunch it was related to me updating the last_modified timestamp after updating a bunch of countries, regions, etc in items
  • Then today I noticed this option in dspace.cfg: eperson.subscription.onlynew
  • By default DSpace sends notifications for modified items too! I've disabled it now...