cgspace-notes/content/posts/2023-01.md

title	date	author	categories
January, 2023	2023-01-01T08:44:36+03:00	Alan Orth	Notes

2023-01-01

• Apply some more ORCID identifiers to items on CGSpace using my 2022-09-22-add-orcids.csv file
  • I want to update all ORCID names and refresh them in the database
  • I see we have some new ones that aren't in our list if I combine with this file:

$ cat 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                         
1939
$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml 2022-09-22-add-orcids.csv| grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u | wc -l
1973

• I will extract and process them with my resolve-orcids.py script:

$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml 2022-09-22-add-orcids.csv| grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2023-01-01-orcids.txt
$ ./ilri/resolve-orcids.py -i /tmp/2023-01-01-orcids.txt -o /tmp/2023-01-01-orcids-names.txt -d

$ ./ilri/update-orcids.py -i /tmp/2023-01-01-orcids-names.txt -db dspace -u dspace -p 'fuuu' -m 247

• Load on CGSpace is high around 9.x
  • I see there is a CIAT bot harvesting via the REST API with IP 45.5.186.2
  • Other than that I don't see any particular system stats as alarming
  • There has been a marked increase in load in the last few weeks, perhaps due to Initiative activity...
  • Perhaps there are some stuck PostgreSQL locks from CLI tools?

$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
     58 dspaceCli
     46 dspaceWeb

• The current time on the server is 08:52 and I see the dspaceCli locks were started at 04:00 and 05:00... so I need to check which cron jobs those belong to as I think I noticed this last month too
  • I'm going to wait and see if they finish, but by tomorrow I will kill them