cgspace-notes/content/posts/2023-06.md

title	date	author	categories
June, 2023	2023-06-02T10:29:36+03:00	Alan Orth	Notes

2023-06-02

• Spend some time testing my post_bitstreams.py script to update thumbnails for items on CGSpace
  • Interestingly I found an item with a JFIF thumbnail and another with a WebP thumbnail...
• Meeting with Valentina, Stefano, and Sara about MODS metadata in CGSpace
  • They have experience with improving the MODS interface in MELSpace's OAI-PMH for use with AGRIS and were curious if we could do the same in CGSpace
  • From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then just add a bunch of our fields to the crosswalk

2023-06-04

• Upgrade CGSpace to Ubuntu 22.04
  • The upgrade was mostly normal, but I had to unhold the openjdk package in order for do-release-upgrade to run:

# apt-mark hold openjdk-8-jdk-headless:amd64 openjdk-8-jre-headless:amd64

• In [2022-11]({{< relref "2022-11.md" >}}) an upstream Java update broke the DSpace 6 Handle server so we will have to pin this again after the upgrade to Ubuntu 22.04
• After the upgrade I made sure CGSpace was working, then proceeded to upgrade PostgreSQL from 12 to 14, like I did on [DSpace Test in 2023-03]({{< relref "2023-03.md" >}})
• Then I had to downgrade OpenJDK to fix the Handle server using the ones I had previously downloaded for Ubuntu 20.04 because they no longer exist on Launchpad:

# dpkg -i openjdk-8-j*8u342-b07*.deb

• Export CGSpace to fix missing Initiative collection mappings
• Start a harvest on AReS
• Work on the DSpace 7 migration a bit more
  • I decided to rebase and drop all the submission form edits because they conflict every time upstream changes!

2023-06-06

• Fix some incorrect ORCID identifiers for an Alliance author on CGSpace
• Export our list of ORCID identifiers, resolve them, and update the records in CGSpace:

$ 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/2023-06-06-orcids.txt
$ ./ilri/resolve_orcids.py -i /tmp/2023-06-06-orcids.txt -o /tmp/2023-06-06-orcids-names.txt -d
$ ./ilri/update_orcids.py -i /tmp/2023-06-06-orcids-names.txt -db dspacetest -u dspace -p 'ffff' -m 247

• Start working on updating the MODS schema in CGSpace from 3.1 to 3.8 based on Stefano and Salem's work last year

2023-06-08

• Continue working on the MODS schema mapping
• Export CGSpace to check and update dcterms.extent fields
  • I normalized about 1,500 to use either "p. 1-6" or "5 p." format
  • Also, I used this GREL expression to extract missing pages from the citation field: cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*(pp?\.\s?\d+[-–]\d+).*/)[0]
  • This was over 4,000 items with a format like "p. 1-6" and "pp. 1-6" in the citation
  • I used another GREL expression to extract another 5,000: cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*?(\d+\s+?[Pp]+\.).*/)[0]
  • This was for the format like "1 p." (note we had to protect against the greedy .* in the beginning)
• I also did some work to capture a handful of missing DOIs and ISSNs, but it was only about 100 items and I will have to wait until the 10,000+ above finish importing

2023-06-09

• I see there are ~200 users in CGSpace that have registered with their CGIAR email address using a password as opposed to using Active Directory:

SELECT * FROM eperson WHERE email LIKE '%cgiar.org' AND netid IS NOT NULL AND password IS NOT NULL;

• I am wondering if I should delete their passwords and tell them use log in using LDAP
  • As an initial test I will reset a few accounts including my own that have passwords and salts:

UPDATE eperson SET password=DEFAULT,salt=DEFAULT,digest_algorithm=DEFAULT WHERE netid IN ('axxxx', 'axxxx', 'bxxxx');

• I also decided to reset passwords/salts for CGIAR accounts that have not been active since 2021 (1.5 years ago):

UPDATE eperson  SET password=DEFAULT,salt=DEFAULT,digest_algorithm=DEFAULT WHERE email LIKE '%cgiar.org' AND netid IS NOT NULL AND password IS NOT NULL AND salt IS NOT NULL AND last_active < '2022-01-01'::date;

• This was about 100 accounts...
  • I will wait some more time before I decide what to do about the more current ones
• Add a few more ORCID identifiers to my list and tag them on CGSpace

2023-06-10

• Export CGSpace to check for missing Initiative mappings
  • Start a harvest on AReS

2023-06-11

• File an issue on DSpace for the Content-Disposition bug causing images to get downloaded instead of opened inline

2023-06-12

• Export CGSpace to do some more work extracting volume and issue from citations for items where they are missing
  • I found and fixed over 7,000!
  • Then I found and extracted another 7,000 items with no extents (pages)
  • Then I replaced all occurences of en dashes for ranges in pages with regular hyphens

2023-06-13

• Last night I finally figured out how to do basic overrides to the simple item view in Angular
• Add a handful of new ORCID identifiers to my list and tag them on CGSpace
• Extract a list of all the proposed actions for CG Core output types and create a new issue for them on CG Core's GitHub repository
• Extract a list of all the proposed actions for CG Core output types for MARLO and create a new issue for them on MARLO's GitHub repository
• Meeting with Indira, Ryan, and Abenet to discuss plans for the DSpace 7 focus group

2023-06-14

• Did some more work on the DSpace 7 Test to improve the submission forms and the look and feel
• Extract a list of all the proposed actions for CG Core output types for MEL and create a new issue for them on MEL's GitHub repository