CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

May, 2024

in  Notes

2024-05-01

  • I dumped all the CGSpace DOIs and resolved them with my crossref_doi_lookup.py script
    • Then I did some work to add missing abstracts (about 900!), volumes, issues, licenses, publishers, and types, etc

2024-05-05

  • Spend some time looking at duplicate DOIs again…

2024-05-06

  • Spend some time looking at duplicate DOIs again…

2024-05-07

$ zstdgrep -a 'URI Too Long' log/dspace.log-2024-04-* | wc -l
1423
  • Spend some time looking at duplicate DOIs again…

2024-05-08

  • Spend some time looking at duplicate DOIs again…
    • I finally finished looking at the duplicate DOIs for journal articles
    • I updated the list of handle redirects and there are 386 of them!

2024-05-09

  • Spend some time working on the IFPRI 2020–2021 batch
    • I started by checking for exact duplicates (1.0 similarity) using DOI, type, and issue date

2024-05-12

  • I couldn’t figure out how to do a complex join on withdrawn items along with their metadata, so I pull out a few like titles, handles, and provenance separately:
dspace=# \COPY (SELECT i.uuid, m.text_value AS uri FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=25) TO /tmp/withdrawn-handles.csv CSV HEADER;
dspace=# \COPY (SELECT i.uuid, m.text_value AS title FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=64) TO /tmp/withdrawn-titles.csv CSV HEADER;
dspace=# \COPY (SELECT i.uuid, m.text_value AS submitted_by FROM item i JOIN metadatavalue m ON i.uuid = m.dspace_object_id WHERE withdrawn AND m.metadata_field_id=28 AND m.text_value LIKE 'Submitted by%') TO /tmp/withdrawn-submitted-by.csv CSV HEADER;
  • Then joined them:
$ csvjoin -c uuid /tmp/withdrawn-title.csv /tmp/withdrawn-handles.csv /tmp/withdrawn-submitted-by.csv > /tmp/withdrawn.csv
  • This gives me an insight into who submitted at 334 of the duplicates over the past few years…
  • I fixed a few hundred titles with leading/trailing whitespace, newlines, and ligatures like ff, fi, fl, ffi, and ffl

2024-05-13

  • Export a list of IFPRI information products with handle links and CONTENTdm links:
$ csvgrep -c 'dc.description.provenance[en_US]' -m 'CONTENTdm' cgspace.csv \
  | csvcut -c 'id,dc.description.provenance[en_US],dc.identifier.uri[en_US]' \
  | tee /tmp/ifpri-redirects.csv \
  | csvstat --count
2645
  • I discovered the /server/api/pid/find endpoint today, which is much more direct and manageable than the /server/api/discover/search/objects?query= endpoint when trying to get metadata for a Handle (item, collection, or community)
    • The “pid” stands for permanent identifiers apparently, and we can use it like this:
https://dspace7test.ilri.org/server/api/pid/find?id=10568/118424

2024-05-15

  • I got journal titles for 2,900 journal articles that were missing them from Crossref

2024-05-16

Helping IFPRI with some DSpace 7 API support, these are two queries for items issued in 2024:

Both of them return the same number of results and seem identitical as far as I can see, but the second one uses Solr date indexes and requires the full Lucene datetime and range syntax

I wrote a new version of the check_duplicates.py script to help identify duplicates with different types

  • Initially I called it check_duplicates_fast.py but it’s actually not faster
  • I need to find a way to deal with duplicates from IFPRI’s repository because there are some mismatched types…

2024-05-20

Continue working through alternative duplicate matching for IFPRI

  • Their item types are sometimes different than ours…
  • One thing I think I can say for sure is that the default similarity factor in my script is 0.6, and I rarely see legitimate duplicates with such similarity so I might increase this to 0.7 to reduce the number of items I have to check
  • Also, the difference in issue dates is currently 365, but I should reduce that a bit, perhaps to 270 days (9 months)