CGSpace Notes

2024-03-01

• Last week Bizu reported an issue with the “browse by issue date” drop down
  • I verified it, and suspect it could be due to missing issue dates…
  • It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808

• I spent some time trying to reproduce the bug affecting onebox fields that are configured to use external vocabularies and are not repeatable
  • I filed an issue: https://github.com/DSpace/dspace-angular/issues/2846

2024-03-03

• I did some cleanups on abstracts, licenses, and dates from CrossRef
• I also did some minor cleanups to affiliations because I saw some incorrect and duplicate ones in our list

2024-03-05

• I tried a new technique to get some affiliations from Crossref using OpenRefine
  • First I split them and clustered, resolving a few hundred clusters out of 1500 (!)
  • Then I used a custom text facet with a few dozen CGIAR and other large affiliations to reduce the work
  • Then I joined them with our affiliations, paying no attention to duplicates
  • Then I deduped them using the Jython technique I learned in 2023-02

2024-03-06

• Peter sent me some more corrections for the authors that I had sent him in 2023-12

2024-03-08

• IFPRI sent me their 2023 records from CONTENTdm so I started working on those
  • I found a way to match their ORCID identifiers in our list using Jython in OpenRefine:

import re

with open(r"/tmp/cg-creator-identifier.txt",'r') as f :
    orcid_ids = [orcid_id.strip() for orcid_id in f]

matched = False
for orcid_id in orcid_ids:
    if re.search(r'.+: {}'.format(value), orcid_id):
        matched = True
        break

if matched:
    return orcid_id
else:
    return value

• I realized that UNICEF was renamed to its current name in 1953 so I replaced all other variations in our vocabularies and metadata:

UPDATE metadatavalue SET text_value='United Nations Children''s Fund' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value IN ('United Nations International Children''s Emergency Fund', 'United Nations International Children''s Emergency Fund', 'UNICEF');

• Note the use of two single quotes to escape the one in the name

2024-03-11

• Experimenting with moving some of my Python scripts to the DSpace 7 REST API
  • I need a way to get UUIDs for Handles…
  • Seems that I can use a Discovery query like: https://dspace7test.ilri.org/server/api/discover/search/objects?dsoType=item&query=handle:10568/130864
  • Then just take the first result…?
• I spent some time working on the script get abstracts from CGSpace, and found a bug in my logic
  • I also noticed that one item had two abstracts, but the first one was blank!
  • Looking deeper, I found 113 blank metadata values so I deleted those:

BEGIN;
DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='';
COMMIT;

• I also found a few dozen items with “N/A” for their citation, so I deleted those too:

BEGIN;
DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='N/A' AND metadata_field_id=146;
COMMIT;

• I deployed the change to disable Angular SSR’s inlineCriticalCss on production because we had heavy load on the frontend and I’ve been meaning to do this permanently for some time
• Maria asked me for a CSV with all the broken Bioversity permalinks so I exported them for her:

$ csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],cg.link.permalink[en_US]' ~/Downloads/2024-03-05-cgspace.csv \
  | csvgrep -c 'cg.link.permalink[en_US]' -r '^.+$' > /tmp/2024-03-11-Bioversity-Permalinks.csv