## March, 2024

Fri Mar 01, 2024 in 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

## 2024-03-12

- Run the duplicate checker for IFPRI 2023 batch upload

## 2024-03-13

- I found about 428 duplicates in the IFPRI 2023 batch records
  - Alarmingly, I found about 18 that are duplicated on CGSpace as well!
  - I looked closer and decided that 11 were duplicates, so I merged the metadata and withdrew the later ones
- Alliance asked me to get him the Handles for items submitted by TIP that are not discoverable
  - I found it easiest to use the `ds6_item2itemhandle` DSpace SQL helper function with a nested query on the provenance:

    SELECT ds6_item2itemhandle(dspace_object_id) AS handle FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item WHERE NOT discoverable) AND metadata_field_id=28 AND text_value LIKE 'Submitted by Alliance TIP Submit%';

## 2024-03-14

- Looking in to reports of rate limiting of Altmetric’s bot on CGSpace
  - I don’t see any HTTP 429 responses for their user agents in any of our logs…
  - I tried myself on an item page and never hit a limit…

    $ for num in {1..60}; do echo -n "Request ${num}: "; curl -s -o /dev/null -w "%{http_code}" https://dspace7test.ilri.org/items/c9b8999d-3001-42ba-a267-14f4bfa90b53 && echo; done
    Request 1: 200
    Request 2: 200
    Request 3: 200
    Request 4: 200
    ...
    Request 60: 200

- All responses were HTTP 200…
- In any case, I whitelisted their production IPs and told them to try again
- I imported 468 of IFPRI’s 2023 records that were confirmed to not be duplicates to CGSpace
  - I also spent some time merging metadata from 415 of the remaining 432 duplicates with the metadata for the existing items on CGSpace
  - This was a bit of dirty work using csvkit, xsv, and OpenRefine

## 2024-03-17

- There are 17 records from IFPRI’s 2023 batch that are remaining from the 432 that I identified as already being on CGSpace
  - These are different in that they are duplicates on CGSpace as well, so the csvjoin failed and the metadata got messed up in my migration
  - I looked closer and whittled this down to 14 actual records, and spent some time working on them
  - I isolated 12 of these items that existed on CGSpace and added publication ranks, project identifiers, and provenance links
  - Now there only remain two confusing records about the Inkomati catchment

## 2024-03-18

- Checking to see how many IFPRI records we have migrated so far:

    $ csvgrep -c 'dc.description.provenance[en_US]' -m 'Original URL from IFPRI CONTENTdm' cgspace.csv \
      | csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],dc.description.provenance[en_US],dcterms.type[en_US]' \
      | tee /tmp/ifpri-records.csv \
      | csvstat --count
    898

- I finalized the remaining two on Inkomati catchment and now we are at 900!

# 2024-03-19

- IWMI sent me some new author ORCID identifiers so I updated our list
- Started working on updating my data for the Ontology CoP webinar on CGIAR and AGROVOC
  - First extracting all unique subjects on CGSpace:

    localhost/dspace7= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS "subject" FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119)) to /tmp/2024-03-19-cgspace-subjects.csv WITH CSV HEADER;
    COPY 28024

- Then I extracted the subjects and looked them up against AGROVOC:

    $ csvcut -c subject /tmp/2024-03-19-cgspace-subjects.csv | sed '1d' > /tmp/2024-03-19-cgspace-subjects.txt
    $ ./ilri/agrovoc_lookup.py -i /tmp/2024-03-19-cgspace-subjects.txt -o /tmp/2024-03-19-cgspace-subjects-results.csv

## 2024-03-20

- Identify seven duplicates on CGSpace from the PRMS results and withdraw them from CGSpace

## 2024-03-21

- Look more closely at duplicates on CGSpace based on a fresh export
  - Using DOIs I found ~842 that occur more than once for journal articles alone, so probably around 400 duplicates
  - I did a handful of them, merging the metadata and withdrawing the duplicate, and decided to add `dcterms.replaces` with the handle in the original

## 2024-03-22

- Look at duplicate DOIs on CGSpace and address a dozen or so

## 2024-03-23

- Look at duplicate DOIs on CGSpace and address a dozen or so
- Update Tomcat and Solr to latest versions
  - I had done some tests with these last week, and did a last minute test on DSpace 7 Test to make sure submission and searching worked

## 2024-03-24

- Slowly process several dozen more duplicate DOIs on CGSpace, sigh…